Effectors of innate immunity determination

ABSTRACT

A method of identifying a polynucleotide or pattern of polynucleotides regulated by one or more sepsis or inflammatory inducing agents and inhibited by a peptide is described. A method of identifying a pattern of polynucleotide expression for inhibition of an inflammatory or septic response. The method includes contacting cells with LPS, LTA, CpG DNA and/or intact microbe or microbial components in the presence or absence of a cationic peptide; detecting a pattern of polynucleotide expression for the cells in the presence and absence of the peptide, wherein the pattern in the presence of the peptide represents inhibition of an inflammatory or septic response. Also included are compounds and agents identified by the methods of the invention. In another aspect, the invention provides methods and compounds for enhancing innate immunity in a subject.

RELATED APPLICATION DATA

This application claims priority under 35 USC 120 to U.S. patent application Ser. No. 10/308,905, filed Dec. 2, 2002, and under 35 USC 119(e) to U.S. Patent Application Ser. No. 60/336,632, filed Dec. 3, 2001, herein incorporated by reference in their entirety.

FIELD OF THE INVENTION

The present invention relates generally to peptides and specifically to peptides effective as therapeutics and for drug discovery related to pathologies resulting from microbial infections and for modulating innate immunity or anti-inflammatory activity.

BACKGROUND OF THE INVENTION

Infectious diseases are the leading cause of death worldwide. According to a 1999 World Health Organization study, over 13 million people die from infectious diseases each year. Infectious diseases are the third leading cause of death in North America, accounting for 20% of deaths annually and increasing by 50% since 1980. The success of many medical and surgical treatments also hinges on the control of infectious diseases. The discovery and use of antibiotics has been one of the great achievements of modern medicine. Without antibiotics, physicians would be unable to perform complex surgery, chemotherapy or most medical interventions such as catheterization.

Current sales of antibiotics are US$26 billion worldwide. However, the overuse and sometimes unwarranted use of antibiotics have resulted in the evolution of new antibiotic-resistant strains of bacteria. Antibiotic resistance has become part of the medical landscape. Bacteria such as vancomycin-resistant Enterococcus, VRE, and methicillin-resistant Staphylococcus aureus and MRSA, strains cannot be treated with antibiotics and often, patients suffering from infections with such bacteria die. Antibiotic discovery has proven to be one of the most difficult areas for new drug development and many large pharmaceutical companies have cut back or completely halted their antibiotic development programs. However, with the dramatic rise of antibiotic resistance, including the emergence of untreatable infections, there is a clear unmet medical need for novel types of anti-microbial therapies, and agents that impact on innate immunity would be one such class of agents.

The innate immune system is a highly effective and evolved general defense system. Elements of innate immunity are always present at low levels and are activated very rapidly when stimulated. Stimulation can include interaction of bacterial signaling molecules with pattern recognition receptors on the surface of the body's cells or other mechanisms of disease. Every day, humans are exposed to tens of thousands of potential pathogenic microorganisms through the food and water we ingest, the air we breathe and the surfaces, pets and people that we touch. The innate immune system acts to prevent these pathogens from causing disease. The innate immune system differs from so-called adaptive immunity (which includes antibodies and antigen-specific B- and T-lymphocytes) because it is always present, effective immediately, and relatively non-specific for any given pathogen. The adaptive immune system requires amplification of specific recognition elements and thus takes days to weeks to respond. Even when adaptive immunity is pre-stimulated by vaccination, it may take three days or more to respond to a pathogen whereas innate immunity is immediately or rapidly (hours) available. Innate immunity involves a variety of effector functions including phagocytic cells, complement, etc, but is generally incompletely understood. Generally speaking many innate immune responses are “triggered” by the binding of microbial signaling molecules with pattern recognition receptors termed Toll-like receptors on the surface of host cells. Many of these effector functions are grouped together in the inflammatory response. However too severe an inflammatory response can result in responses that are harmful to the body, and in an extreme case sepsis and potentially death can occur.

The release of structural components from infectious agents during infection causes an inflammatory response, which when unchecked can lead to the potentially lethal condition, sepsis. Sepsis occurs in approximately 780,000 patients in North America annually. Sepsis may develop as a result of infections acquired in the community such as pneumonia, or it may be a complication of the treatment of trauma, cancer or major surgery. Severe sepsis occurs when the body is overwhelmed by the inflammatory response and body organs begin to fail. Up to 120,000 deaths occur annually in the United Stated due to sepsis. Sepsis may also involve pathogenic microorganisms or toxins in the blood (e.g., septicemia), which is a leading cause of death among humans. Gram-negative bacteria are the organisms most commonly associated with such diseases. However, gram-positive bacteria are an increasing cause of infections. Gram-negative and Gram-positive bacteria and their components can all cause sepsis.

The presence of microbial components induce the release of pro-inflammatory cytokines of which tumor necrosis factor-α (TNF-α) is of extreme importance. TNF-α and other pro-inflammatory cytokines can then cause the release of other pro-inflammatory mediators and lead to an inflammatory cascade. Gram-negative sepsis is usually caused by the release of the bacterial outer membrane component, lipopolysaccharide (LPS; also referred to as endotoxin). Endotoxin in the blood, called endotoxemia comes primarily from a bacterial infection, and may be released during treatment with antibiotics. Gram-positive sepsis can be caused by the release of bacterial cell wall components such as lipoteichoic acid (LTA), peptidoglycan (PG), rhamnose-glucose polymers made by Streptococci, or capsular polysaccharides made by Staphylococci. Bacterial or other non-mammalian DNA that, unlike mammalian DNA, frequently contains unmethylated cytosine-guanosine dimers (CpG DNA) has also been shown to induce septic conditions including the production of TNF-α. Mammalian DNA contains CpG dinucleotides at a much lower frequency, often in a methylated form. In addition to their natural release during bacterial infections, antibiotic treatment can also cause release of the bacterial cell wall components LPS and LTA and probably also bacterial DNA. This can then hinder recovery from infection or even cause sepsis.

Cationic peptides are being increasingly recognized as a form of defense against infection, although the major effects recognized in the scientific and patent literature are the antimicrobial effects (Hancock, R. E. W., and R. Lehrer. 1998. Cationic peptides: a new source of antibiotics. Trends in Biotechnology 16:82-88.). Cationic peptides having antimicrobial activity have been isolated from a wide variety of organisms. In nature, such peptides provide a defense mechanism against microorganisms such as bacteria and yeast. Generally, these cationic peptides are thought to exert their antimicrobial activity on bacteria by interacting with the cytoplasmic membrane, and in most cases, forming channels or lesions. In gram-negative bacteria, they interact with LPS to permeabilize the outer membrane, leading to self promoted uptake across the outer membrane and access to the cytoplasmic membrane. Examples of cationic antimicrobial peptides include indolicidin, defensins, cecropins, and magainins.

Recently it has been increasingly recognized that such peptides are effectors in other aspects of innate immunity (Hancock, R. E. W. and G. Diamond. 2000. The role of cationic peptides in innate host defenses. Trends in Microbiology 8:402-410; Hancock, R. E. W. 2001. Cationic peptides: effectors in innate immunity and novel antimicrobials. Lancet Infectious Diseases 1:156-164) although it was not known if the antimicrobial and effector functions are independent.

Some cationic peptides have an affinity for binding bacterial products such as LPS and LTA. Such cationic peptides can suppress cytokine production in response to LPS, and to varying extents can prevent lethal shock. However it has not been proven as to whether such effects are due to binding of the peptides to LPS and LTA, or due to a direct interaction of the peptides with host cells. Cationic peptides are induced, in response to challenge by microbes or microbial signaling molecules like LPS, by a regulatory pathway similar to that used by the mammalian immune system (involving Toll receptors and the transcription factor; NFκB). Cationic peptides therefore appear to have a key role in innate immunity. Mutations that affect the induction of antibacterial peptides can reduce survival in response to bacterial challenge. As well, mutations of the Toll pathway of Drosophila that lead to decreased antifungal peptide expression result in increased susceptibility to lethal fungal infections. In humans, patients with specific granule deficiency syndrome, completely lacking in α-defensins, suffer from frequent and severe bacterial infections. Other evidence includes the inducibility of some peptides by infectious agents, and the very high concentrations that have been recorded at sites of inflammation. Cationic peptides may also regulate cell migration, to promote the ability of leukocytes to combat bacterial infections. For example, two human β-defensin peptides, HNP-1 and HNP-2, have been indicated to have direct chemotactic activity for murine and human T cells and monocytes, and human β-defensins appear to act as chemoattractants for immature dendritic cells and memory T cells through interaction with CCR6. Similarly, the porcine cationic peptide, PR-39 was found to be chemotactic for neutrophils. It is unclear however as to whether peptides of different structures and compositions share these properties.

The single known cathelicidin from humans, LL-37, is produced by myeloid precursors, testis, human keratinocytes during inflammatory disorders and airway epithelium. The characteristic feature of cathelicidin peptides is a high level of sequence identity at the N-terminus prepro regions termed the cathelin domain. Cathelicidin peptides are stored as inactive propeptide precursors that, upon stimulation, are processed into active peptides.

SUMMARY OF THE INVENTION

The present invention is based on the seminal discovery that based on patterns of polynucleotide expression regulated by endotoxic lipopolysaccharide, lipoteichoic acid, CpG DNA, or other cellular components (e.g., microbe or their cellular components), and affected by cationic peptides, one can screen for novel compounds that block or reduce sepsis and/or inflammation in a subject. Further, based on the use of cationic peptides as a tool, one can identify selective enhancers of innate immunity that do not trigger the sepsis reaction and that can block/dampen inflammatory and/or septic responses.

Thus, in one embodiment, a method of identifying a polynucleotide or pattern of polynucleotides regulated by one or more sepsis or inflammatory inducing agents and inhibited by a cationic peptide, is provided. The method of the invention includes contacting the polynucleotide or polynucleotides with one or more sepsis or inflammatory inducing agents and contacting the polynucleotide or polynucleotides with a cationic peptide either simultaneously or immediately thereafter. Differences in expression are detected in the presence and absence of the cationic peptide, and a change in expression, either up- or down-regulation, is indicative of a polynucleotide or pattern of polynucleotides that is regulated by a sepsis or inflammatory inducing agent and inhibited by a cationic peptide. In another aspect the invention provides a polynucleotide or polynucleotides identified by the above method. Examples of sepsis or inflammatory regulatory agents include LPS, LTA or CpG DNA or microbial components (or any combination thereof), or related agents.

In another embodiment, the invention provides a method of identifying an agent that blocks sepsis or inflammation including combining a polynucleotide identified by the method set forth above with an agent wherein expression of the polynucleotide in the presence of the agent is modulated as compared with expression in the absence of the agent and wherein the modulation in expression affects an inflammatory or septic response.

In another embodiment, the invention provides a method of identifying a pattern of polynucleotide expression for inhibition of an inflammatory or septic response by 1) contacting cells with LPS, LTA and/or CpG DNA in the presence or absence of a cationic peptide and 2) detecting a pattern of polynucleotide expression for the cells in the presence and absence of the peptide. The pattern obtained in the presence of the peptide represents inhibition of an inflammatory or septic response. In another aspect the pattern obtained in the presence of the peptide is compared to the pattern of a test compound to identify a compound that provides a similar pattern. In another aspect the invention provides a compound identified by the foregoing method.

In another embodiment, the invention provides a method of identifying an agent that enhances innate immunity by contacting a polynucleotide or polynucleotides that encode a polypeptide involved in innate immunity, with an agent of interest, wherein expression of the polynucleotide in the presence of the agent is modulated as compared with expression of the polynucleotide in the absence of the agent and wherein the modulated expression results in enhancement of innate immunity. Preferably, the agent does not stimulate a sepsis reaction in a subject. In one aspect, the agent increases the expression of an anti-inflammatory polynucleotide. Exemplary, but non-limiting anti-inflammatory polynucleotides encode proteins such as IL-1 R antagonist homolog 1 (AI167887), IL-10 R beta (AA486393), IL-10 R alpha (U00672) TNF Receptor member 1B (AA150416), TNF receptor member 5 (H98636), TNF receptor member 11 b (AA194983), IK cytokine down-regulator of HLA II (R39227), TGF-B inducible early growth response 2 (AI473938), CD2 (AA927710), IL-19 (NM_(—)013371) or IL-10 (M57627). In one aspect, the agent decreases the expression of polynucleotides encoding proteasome subunits involved in NF-κB activation such as proteasome subunit 26S (NM_(—)013371). In one aspect, the agent may act as an antagonist of protein kinases. In one aspect, the agent is a peptide selected from SEQ ID NO:4-54.

In another embodiment, the invention provides a method of identifying a pattern of polynucleotide expression for identification of a compound that selectively enhances innate immunity. The invention includes detecting a pattern of polynucleotide expression for cells contacted in the presence and absence of a cationic peptide, wherein the pattern in the presence of the peptide represents stimulation of innate immunity; detecting a pattern of polynucleotide expression for cells contacted in the presence of a test compound, wherein a pattern with the test compound that is similar to the pattern observed in the presence of the cationic peptide, is indicative of a compound that enhances innate immunity. It is preferred that the compound does not stimulate a septic reaction in a subject.

In another embodiment, the invention provides a method for inferring a state of infection in a mammalian subject from a nucleic acid sample of the subject by identifying in the nucleic acid sample a polynucleotide expression pattern exemplified by an increase in polynucleotide expression of at least 2 polynucleotides in Table 50, 51 and or 52, as compared to a non-infected subject. Also included is a polynucleotide expression pattern obtained by any of the methods described above.

In another aspect a cationic peptide that is an antagonist of CXCR-4 is provided. In still another aspect, a method of identifying a cationic peptide that is an antagonist of CXCR-4 by contacting T cells with SDF-1 in the presence of absence of a test peptide and measuring chemotaxis is provided. A decrease in chemotaxis in the presence of the test peptide is indicative of a peptide that is an antagonist of CXCR-4. Cationic peptide also acts to reduce the expression of the SDF-1 receptor polynucleotide (NM_(—)013371).

In all of the above described methods, the compounds or agents of the invention include but are not limited to peptides, cationic peptides, peptidomimetics, chemical compounds, polypeptides, nucleic acid molecules and the like.

In still another aspect the invention provides an isolated cationic peptide. An isolated cationic peptide of the invention is represented by one of the following general formulas and the single letter amino acid code:

X₁X₂X₃IX₄PX₄IPX₅X₂X₁ (SEQ ID NO: 4), where X₁ is one or two of R, L or K, X₂ is one of C, S or A, X₃ is one of R or P, X₄ is one of A or V and X₅ is one of V or W;

X₁LX₂X₃KX₄X₂X₅X₃PX₃X₁ (SEQ ID NO: 11), where X₁ is one or two of D, E, S, T or N, X₂ is one or two of P, G or D, X₃ is one of G, A, V, L, I or Y, X₄ is one of R, K or H and X₅ is one of S, T, C, M or R;

X₁X₂X₃X₄WX₄WX₄X₅K (SEQ ID NO: 18), where X₁ is one to four chosen from A, P or R, X₂ is one or two aromatic amino acids (F, Y and W), X₃ is one of P or K, X₄ is one, two or none chosen from A, P, Y or W and X₅ is one to three chosen from R or P;

X₁X₂X₃X₄X₁VX₃X₄RGX₄X₃X₄X₁X₃X₁ (SEQ ID NO: 25) where X₁ is one or two of R or K, X₂ is a polar or charged amino acid (S, T, M, N, Q, D, E, K, R and H), X₃ is C, S, M, D or A and X₄ is F, I, V, M or R;

X₁X₂X₃X₄X₁VX₅X₄RGX₄X₅X₄X₁X₃X₁ (SEQ ID NO: 32), where X₁ is one or two of R or K, X₂ is a polar or charged amino acid (S, T, M, N, Q, D, E, K, R and H), X₃ is one of C, S, M, D or A, X₄ is one of F, I, V, M or R and X₅ is one of A, I, S, M, D or R; and

KX₁KX₂FX₂KMLMX₂ALKKX₃ (SEQ ID NO: 39), where X₁ is a polar amino acid (C, S, T, M, N and Q); X₂ is one of A, L, S or K and X₃ is 1-17 amino acids chosen from G, A, V, L, I, P, F, S, T, K and H;

KWKX₂X₁X₁X₂X₂X₁X₂X₂X₁X₁X₂X₂₁FHTALKPISS (SEQ ID NO: 46), where X₁ is a hydrophobic amino acid and X₂ is a hydrophilic amino acid.

Additionally, in another aspect the invention provides isolated cationic peptides KWKSFLRTFKSPVRTVFHTALKPISS (SEQ ID NO: 53) and KWKSYAHTIMSPVRLVFHTALKPISS (SEQ ID NO: 54).

Also provided are nucleic acid sequences encoding the cationic peptides of the invention, vectors including such polynucleotides and host cells containing the vectors.

In another embodiment, the invention provides methods for stimulating or enhancing innate immunity in a subject comprising administering to the subject a peptide of the invention, for example, peptides set forth in SEQ ID NO: 1-4, 11, 18, 25, 32, 39, 46, 53 or 54. As shown in the Examples herein, innate immunity can be evidenced by monocyte activation, proliferation, differentiation or MAP kinase pathway activation just by way of example. In one aspect, the method includes further administering a serum factor such as GM-CSF to the subject. The subject is preferably any mammal and more particularly a human subject.

In another embodiment, the invention provides a method of stimulating innate immunity in a subject having or at risk of having an infection including administering to the subject a sub-optimal concentration of an antibiotic in combination with a peptide of the invention. In one aspect, the peptide is SEQ ID NO:1 or SEQ ID NO:7.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 demonstrates the synergy of Seq ID No: 7 with cefepime in curing S. aureus infections. CD-1 mice (8/group) were given 1×10⁷ S. aureus in 5% porcine mucin via IP injection. Test compound (50 μg-2.5 mg/kg) was given via a separate IP injection 6 hours after S. aureus. At this time Cefepime was also given at a dose of 0.1 mg/kg. Mice were euthanized 24 hr later, blood removed and plated for viable counts. The average±standard error is shown. This experiment was repeated twice.

FIG. 2 shows exposure to SEQ ID NO: 1 induces phosphorylation of ERK1/2 and p38. Lysates from human peripheral blood derived monocytes were exposed to 50 μg/ml of SEQ ID NO: 1 for 15 minutes. A) Antibodies specific for the phosphorylated forms of ERK and p38 were used to detect activation of ERK1/2 and p38. All donors tested showed increased phosphorylation of ERK1/2 and p38 in response to SEQ ID NO: 1 treatment. One representative donor of eight. Relative amounts of phosphorylation of ERK (B) and p38(C) were determined by dividing the intensities of the phosphorylated bands by the intensity of the corresponding control band as described in the Materials and Methods.

FIG. 3 shows LL-37 induced phosphorylation of ERK1/2 does not occur in the absence of serum and the magnitude of phosphorylation is dependent upon the type of serum present. Human blood derived monocytes were treated with 50 μg/ml of LL-37 for 15 minutes. Lysates were run on a 12% acrylamide gel then transferred to nitrocellulose membrane and probed with antibodies specific for the phosphorylated (active) form of the kinase. To normalize for protein loading, the blots were reprobed with β-actin. Quantification was done with ImageJ software. The FIG. 3 inset demonstrates that LL-37 is unable to induce MAPK activation in human monocytes under serum free conditions. Cells were exposed to 50 mg/ml of LL-37 (+), or endotoxin free water (−) as a vehicle control, for 15 minutes. (A) After exposure to LL-37 in media containing 10% fetal calf serum, phosphorylated ERK1/2 was detectable, however, no phosphorylation of ERK1/2 was detected in the absence of serum (n=3). (B) Elk-1, a transcription factor downstream of ERK1/2, was activated (phosphorylated) upon exposure to 50 μg/ml of LL-37 in media containing 10% fetal calf serum, but not in the absence of serum (n=2).

FIG. 4 shows LL-37 induced activation of ERK1/2 occurs at lower concentrations and is amplified in the presence of certain cytokines. When freshly isolated monocytes were stimulated in media containing both GM-CSF (100 ng/ml) and IL-4 (10 ng/ml) LL-37 induced phosphorylation of ERK1/2 was apparent at concentrations as low as 5 μg/ml. This synergistic activation of ERK1/2 seems to be due primarily to GM-CSF.

FIG. 5 shows peptide affects both transcription of various cytokine genes and release of IL-8 in the 16HBE4o-human bronchial epithelial cell line. Cells were grown to confluency on a semi-permeable membrane and stimulated on the apical surface with 50 μg/ml of SEQ ID NO: 1 for four hours. A) SEQ ID NO: 1 treated cells produced significantly more IL-8 than controls, as detected by ELISA in the supernatant collected from the apical surface, but not from the basolateral surface. Mean±SE of three independent experiments shown, asterisk indicates p=0.002. B) RNA was collected from the above experiments and RT-PCR was performed. A number of cytokine genes known to be regulated by either ERK1/2 or p38 were up-regulated upon stimulation with peptide. The average of two independent experiments is shown.

DETAILED DESCRIPTION OF THE INVENTION

The present invention provides novel cationic peptides, characterized by a group of generic formulas, which have ability to modulate (e.g., up- and/or down regulate) polynucleotide expression, thereby regulating sepsis and inflammatory responses and/or innate immunity.

“Innate immunity” as used herein refers to the natural ability of an organism to defend itself against invasions by pathogens. Pathogens or microbes as used herein, may include, but are not limited to bacteria, fungi, parasite, and viruses. Innate immunity is contrasted with acquired/adaptive immunity in which the organism develops a defensive mechanism based substantially on antibodies and/or immune lymphocytes that is characterized by specificity, amplifiability and self vs. non-self dsicrimination. With innate immunity, broad, nonspecific immunity is provided and there is no immunologic memory of prior exposure. The hallmarks of innate immunity are effectiveness against a broad variety of potential pathogens, independence of prior exposure to a pathogen, and immediate effectiveness (in contrast to the specific immune response which takes days to weeks to be elicited). In addition, innate immunity includes immune responses that affect other diseases, such as cancer, inflammatory diseases, multiple sclerosis, various viral infections, and the like.

As used herein, the term “cationic peptide” refers to a sequence of amino acids from about 5 to about 50 amino acids in length. In one aspect, the cationic peptide of the invention is from about 10 to about 35 amino acids in length. A peptide is “cationic” if it possesses sufficient positively charged amino acids to have a pKa greater than 9.0. Typically, at least two of the amino acid residues of the cationic peptide will be positively charged, for example, lysine or arginine. “Positively charged” refers to the side chains of the amino acid residues which have a net positive charge at pH 7.0. Examples of naturally occurring cationic antimicrobial peptides which can be recombinantly produced according to the invention include defensins, cathelicidins, magainins, melittin, and cecropins, bactenecins, indolicidins, polyphemusins, tachyplesins, and analogs thereof. A variety of organisms make cationic peptides, molecules used as part of a non-specific defense mechanism against microorganisms. When isolated, these peptides are toxic to a wide variety of microorganisms, including bacteria, fungi, and certain enveloped viruses. While cationic peptides act against many pathogens, notable exceptions and varying degrees of toxicity exist. However this patent reveals additional cationic peptides with no toxicity towards microorganisms but an ability to protect against infections through stimulation of innate immunity, and this invention is not limited to cationic peptides with antimicrobial activity. In fact, many peptides useful in the present invention do not have antimicrobial activity.

Cationic peptides known in the art include for example, the human cathelicidin LL-37, and the bovine neutrophil peptide indolicidin and the bovine variant of bactenecin, Bac2A.

LL-37 LLGDFFRKSKEKIGKEFKRIVQRI (SEQ ID NO: 1) KDFLRNLVPRTES Indolicidin ILPWKWPWWPWRR-NH₂ (SEQ ID NO: 2) Bac2A RLARIVVIRVAR-NH₂ (SEQ ID NO: 3)

In innate immunity, the immune response is not dependent upon antigens. The innate immunity process may include the production of secretory molecules and cellular components as set forth above. In innate immunity, the pathogens are recognized by receptors encoded in the germline. These Toll-like receptors have broad specificity and are capable of recognizing many pathogens. When cationic peptides are present in the immune response, they aid in the host response to pathogens. This change in the immune response induces the release of chemokines, which promote the recruitment of immune cells to the site of infection.

Chemokines, or chemoattractant cytokines, are a subgroup of immune factors that mediate chemotactic and other pro-inflammatory phenomena (See, Schall, 1991, Cytokine 3:165-183). Chemokines are small molecules of approximately 70-80 residues in length and can generally be divided into two subgroups, α which have two N-terminal cysteines separated by a single amino acid (CxC) and β which have two adjacent cysteines at the N terminus (CC). RANTES, MIP-1α and MIP-1β are members of the β subgroup (reviewed by Horuk, R., 1994, Trends Pharmacol. Sci, 15:159-165; Murphy, P. M., 1994, Annu. Rev. Immunol., 12:593-633). The amino terminus of the β chemokines RANTES, MCP-1, and MCP-3 have been implicated in the mediation of cell migration and inflammation induced by these chemokines. This involvement is suggested by the observation that the deletion of the amino terminal 8 residues of MCP-1, amino terminal 9 residues of MCP-3, and amino terminal 8 residues of RANTES and the addition of a methionine to the amino terminus of RANTES, antagonize the chemotaxis, calcium mobilization and/or enzyme release stimulated by their native counterparts (Gong et al., 1996 J. Biol. Chem. 271:10521-10527; Proudfoot et al., 1996 J. Biol. Chem. 271:2599-2603). Additionally, α chemokine-like chemotactic activity has been introduced into MCP-1 via a double mutation of Tyr 28 and Arg 30 to leucine and valine, respectively, indicating that internal regions of this protein also play a role in regulating chemotactic activity (Beall et al., 1992, J. Biol. Chem. 267:3455-3459).

The monomeric forms of all chemokines characterized thus far share significant structural homology, although the quaternary structures of α and β groups are distinct. While the monomeric structures of the β and α chemokines are very similar, the dimeric structures of the two groups are completely different. An additional chemokine, lymphotactin, which has only one N terminal cysteine has also been identified and may represent an additional subgroup (γ) of chemokines (Yoshida et al., 1995, FEBS Lett. 360:155-159; and Kelner et al., 1994, Science 266:1395-1399).

Receptors for chemokines belong to the large family of G-protein coupled, 7 transmembrane domain receptors (GCR's) (See, reviews by Horuk, R., 1994, Trends Pharmacol. Sci. 15:159-165; and Murphy, P. M., 1994, Annu. Rev. Immunol. 12:593-633). Competition binding and cross-desensitization studies have shown that chemokine receptors exhibit considerable promiscuity in ligand binding. Examples demonstrating the promiscuity among β chemokine receptors include: CC CKR-1, which binds RANTES and MIP-1α (Neote et al., 1993, Cell 72:415-425), CC CKR-4, which binds RANTES, MIP-1α, and MCP-1 (Power et al., 1995, J. Biol. Chem. 270:19495-19500), and CC CKR-5, which binds RANTES, MIP-1α, and MIP-1β (Alkhatib et al., 1996, Science, in press and Dragic et al., 1996, Nature 381:667-674). Erythrocytes possess a receptor (known as the Duffy antigen) which binds both a and P chemokines (Horuk et al., 1994, J. Biol. Chem. 269:17730-17733; Neote et al., 1994, Blood 84:44-52; and Neote et al., 1993, J. Biol. Chem. 268:12247-12249). Thus the sequence and structural homologies evident among chemokines and their receptors allows some overlap in receptor-ligand interactions.

In one aspect, the present invention provides the use of compounds including peptides of the invention to reduce sepsis and inflammatory responses by acting directly on host cells. In this aspect, a method of identification of a polynucleotide or polynucleotides that are regulated by one or more sepsis or inflammatory inducing agents is provided, where the regulation is altered by a cationic peptide. Such sepsis or inflammatory inducing agents include, but are not limited to endotoxic lipopolysaccharide (LPS), lipoteichoic acid (LTA) and/or CpG DNA or intact bacteria or other bacterial components. The identification is performed by contacting the polynucleotide or polynucleotides with the sepsis or inflammatory inducing agents and further contacting with a cationic peptide either simultaneously or immediately after. The expression of the polynucleotide in the presence and absence of the cationic peptide is observed and a change in expression is indicative of a polynucleotide or pattern of polynucleotides that is regulated by a sepsis or inflammatory inducing agent and inhibited by a cationic peptide. In another aspect, the invention provides a polynucleotide identified by the method.

Once identified, such polynucleotides will be useful in methods of screening for compounds that can block sepsis or inflammation by affecting the expression of the polynucleotide. Such an effect on expression may be either up regulation or down regulation of expression. By identifying compounds that do not trigger the sepsis reaction and that can block or dampen inflammatory or septic responses, the present invention also presents a method of identifying enhancers of innate immunity. Additionally, the present invention provides compounds that are used or identified in the above methods.

Candidate compounds are obtained from a wide variety of sources including libraries of synthetic or natural compounds. For example, numerous means are available for random and directed synthesis of a wide variety of organic compounds and biomolecules, including expression of randomized oligonucleotides and oligopeptides. Alternatively, libraries of natural compounds in the form of bacterial, fungal, plant and animal extracts are available or readily produced. Additionally, natural or synthetically produced libraries and compounds are readily modified through conventional chemical, physical and biochemical means, and may be used to produce combinatorial libraries. Known pharmacological agents may be subjected to directed or random chemical modifications, such as acylation, alkylation, esterification, amidification, and the like to produce structural analogs. Candidate agents are also found among biomolecules including, but not limited to: peptides, peptidiomimetics, saccharides, fatty acids, steroids, purines, pyrimidines, polypeptides, polynucleotides, chemical compounds, derivatives, structural analogs or combinations thereof.

Incubating components of a screening assay includes conditions which allow contact between the test compound and the polynucleotides of interest. Contacting includes in solution and in solid phase, or in a cell. The test compound may optionally be a combinatorial library for screening a plurality of compounds. Compounds identified in the method of the invention can be further evaluated, detected, cloned, sequenced, and the like, either in solution or after binding to a solid support, by any method usually applied to the detection of a compound.

Generally, in the methods of the invention, a cationic peptide is utilized to detect and locate a polynucleotide that is essential in the process of sepsis or inflammation. Once identified, a pattern of polynucleotide expression may be obtained by observing the expression in the presence and absence of the cationic peptide. The pattern obtained in the presence of the cationic peptide is then useful in identifying additional compounds that can inhibit expression of the polynucleotide and therefore block sepsis or inflammation. It is well known to one of skill in the art that non-peptidic chemicals and peptidomimetics can mimic the ability of peptides to bind to receptors and enzyme binding sites and thus can be used to block or stimulate biological reactions. Where an additional compound of interest provides a pattern of polynucleotide expression similar to that of the expression in the presence of a cationic peptide, that compound is also useful in the modulation of sepsis or an innate immune response. In this manner, the cationic peptides of the invention, which are known inhibitors of sepsis and inflammation and enhancers of innate immunity are useful as tools in the identification of additional compounds that inhibit sepsis and inflammation and enhance innate immunity.

As can be seen in the Examples below, peptides of the invention have a widespread ability to reduce the expression of polynucleotides regulated by LPS. High levels of endotoxin in the blood are responsible for many of the symptoms seen during a serious infection or inflammation such as fever and an elevated white blood cell count. Endotoxin is a component of the cell wall of Gram-negative bacteria and is a potent trigger of the pathophysiology of sepsis. The basic mechanisms of inflammation and sepsis are related. In Example 1, polynucleotide arrays were utilized to determine the effect of cationic peptides on the transcriptional response of epithelial cells. Specifically, the effects on over 14,000 different specific polynucleotide probes induced by LPS were observed. The tables show the changes seen with cells treated with peptide compared to control cells. The resulting data indicated that the peptides have the ability to reduce the expression of polynucleotides induced by LPS.

Example 2, similarly, shows that peptides of the invention are capable of neutralizing the stimulation of immune cells by Gram positive and Gram negative bacterial products. Additionally, it is noted that certain pro-inflammatory polynucleotides are down-regulated by cationic peptides, as set forth in table 24 such as TLR1 (AI339155), TLR2 (T57791), TLR5 (N41021), TNF receptor-associated factor 2 (T55353), TNF receptor-associated factor 3 (AA504259), TNF receptor superfamily, member 12 (W71984), TNF receptor superfamily, member 17 (AA987627), small inducible cytokine subfamily B, member 6 (AI889554), IL-12R beta 2 (AA977194), IL-18 receptor 1 (AA482489), while anti-inflammatory polynucleotides are up-regulated by cationic peptides, as seen in table 25 such as IL-1 R antagonist homolog 1 (AI167887), IL-10 R beta (AA486393), TNF Receptor member 1B (AA150416), TNF receptor member 5 (H98636), TNF receptor member 11b (AA194983), IK cytokine down-regulator of HLA II (R39227), TGF-B inducible early growth response 2 (AI473938), or CD2 (AA927710). The relevance and application of these results are confirmed by an in vivo application to mice.

In another aspect, the invention provides a method of identifying an agent that enhances innate immunity. In the method, a polynucleotide or polynucleotides that encode a polypeptide involved in innate immunity is contacted with an agent of interest. Expression of the polynucleotide is determined, both in the presence and absence of the agent. The expression is compared and of the specific modulation of expression was indicative of an enhancement of innate immunity. In another aspect, the agent does not stimulate a septic reaction as revealed by the lack of upregulation of the pro-inflammatory cytokine TNF-α. In still another aspect the agent reduces or blocks the inflammatory or septic response. In yet another aspect, the agent reduces the expression of TNF-α and/or interleukins including, but not limited to, IL-1β, IL-6, IL-12 p40, IL-12 p70, and IL-8.

In another aspect, the invention provides methods of direct polynucleotide regulation by cationic peptides and the use of compounds including cationic peptides to stimulate elements of innate immunity. In this aspect, the invention provides a method of identification of a pattern of polynucleotide expression for identification of a compound that enhances innate immunity. In the method of the invention, an initial detection of a pattern of polynucleotide expression for cells contacted in the presence and absence of a cationic peptide is made. The pattern resulting from polynucleotide expression in the presence of the peptide represents stimulation of innate immunity. A pattern of polynucleotide expression is then detected in the presence of a test compound, where a resulting pattern with the test compound that is similar to the pattern observed in the presence of the cationic peptide is indicative of a compound that enhances innate immunity. In another aspect, the invention provides compounds that are identified in the above methods. In another aspect, the compound of the invention stimulates chemokine or chemokine receptor expression. Chemokine or chemokine receptors may include, but are not limited to CXCR4, CXCR1, CXCR2, CCR2, CCR4, CCR5, CCR6, MIP-1 alpha, MDC, MIP-3 alpha, MCP-1, MCP-2, MCP-3, MCP-4, MCP-5, and RANTES. In still another aspect, the compound is a peptide, peptidomimetic, chemical compound, or a nucleic acid molecule.

In still another aspect the polynucleotide expression pattern includes expression of pro-inflammatory polynucleotides. Such pro-inflammatory polynucleotides may include, but are not limited to, ring finger protein 10 (D87451), serine/threonine protein kinase MASK (AB040057), KIAA0912 protein (AB020719), KIAA0239 protein (D87076), RAP1, GTPase activating protein 1 (M64788), FEM-1-like death receptor binding protein (AB007856), cathepsin S (M90696), hypothetical protein FLJ20308 (AK000315), pim-1 oncogene (M54915), proteasome subunit beta type 5 (D29011), KIAA0239 protein (D87076), mucin 5 subtype B tracheobronchial (AJ001403), cAMP response element-binding protein CREBPa, integrin alpha M (J03925), Rho-associated kinase 2 (NM 004850), PTD017 protein (AL050361) unknown genes (AK00143, AK034348, AL049250, AL16199, AL031983) and any combination thereof. In still another aspect the polynucleotide expression pattern includes expression of cell surface receptors that may include but is not limited to retinoic acid receptor (X06614), G protein-coupled receptors (Z94155, X81892, U52219, U22491, AF015257, U66579) chemokine (C-C motif) receptor 7 (L31584), tumor necrosis factor receptor superfamily member 17 (Z29575), interferon gamma receptor 2 (U05875), cytokine receptor-like factor 1 (AF059293), class I cytokine receptor (AF053004), coagulation factor II (thrombin) receptor-like 2 (U92971), leukemia inhibitory factor receptor (NM_(—)002310), interferon gamma receptor 1 (AL050337).

In Example 4 it can be seen that the cationic peptides of the invention alter polynucleotide expression in macrophage and epithelial cells. The results of this example show that pro-inflammatory polynucleotides are down-regulated by cationic peptides (Table 24) whereas anti-inflammatory polynucleotides are up-regulated by cationic peptides (Table 25).

It is shown below, for example, in tables 1-15, that cationic peptides can neutralize the host response to the signaling molecules of infectious agents as well as modify the transcriptional responses of host cells, mainly by down-regulating the pro-inflammatory response and/or up-regulating the anti-inflammatory response. Example 5 shows that the cationic peptides can aid in the host response to pathogens by inducing the release of chemokines, which promote the recruitment of immune cells to the site of infection. The results are confirmed by an in vivo application to mice.

It is seen from the examples below that cationic peptides have a substantial influence on the host response to pathogens in that they assist in regulation of the host immune response by inducing selective pro-inflammatory responses that for example promote the recruitment of immune cells to the site of infection but not inducing potentially harmful pro-inflammatory cytokines. Sepsis appears to be caused in part by an overwhelming pro-inflammatory response to infectious agents. Cationic peptides aid the host in a “balanced” response to pathogens by inducing an anti-inflammatory response and suppressing certain potentially harmful pro-inflammatory responses.

In Example 7, the activation of selected MAP kinases was examined, to study the basic mechanisms behind the effects of interaction of cationic peptides with cells. Macrophages activate MEK/ERK kinases in response to bacterial infection. MEK is a MAP kinase kinase that when activated, phosphorylates the downstream kinase ERK (extracellular regulated kinase), which then dimerizes and translocates to the nucleus where it activates transcription factors such as Elk-1 to modify polynucleotide expression. MEK/ERK kinases have been shown to impair replication of Salmonella within macrophages. Signal transduction by MEK kinase and NADPH oxidase may play an important role in innate host defense against intracellular pathogens. By affecting the MAP kinases as shown below the cationic peptides have an effect on bacterial infection. The cationic peptides can directly affect kinases. Table 21 demonstrates but is not limited to MAP kinase polynucleotide expression changes in response to peptide. The kinases include MAP kinase kinase 6 (H070920), MAP kinase kinase 5 (W69649), MAP kinase 7 (H39192), MAP kinase 12 (AI936909) and MAP kinase-activated protein kinase 3 (W68281).

In another method, the methods of the invention may be used in combination, to identify an agent with multiple characteristics, i.e. a peptide with anti-inflammatory/anti-sepsis activity, and the ability to enhance innate immunity, in part by inducing chemokines in vivo.

In another aspect, the invention provides a method for inferring a state of infection in a mammalian subject from a nucleic acid sample of the subject by identifying in the nucleic acid sample a polynucleotide expression pattern exemplified by an increase in polynucleotide expression of at least 2 polynucleotides in Table 55 as compared to a non-infected subject. In another aspect the invention provides a method for inferring a state of infection in a mammalian subject from a nucleic acid sample of the subject by identifying in the nucleic acid sample a polynucleotide expression pattern exemplified by a polynucleotide expression of at least 2 polynucleotides in Table 56 or Table 57 as compared to a non-infected subject. In one aspect of the invention, the state of infection is due to infectious agents or signaling molecules derived therefrom, such as, but not limited to, Gram negative bacteria and Gram positive bacteria, viral, fungal or parasitic agents. In still another aspect the invention provides a polynucleotide expression pattern of a subject having a state of infection identified by the above method. Once identified, such polynucleotides will be useful in methods of diagnosis of a condition associated with the activity or presence of such infectious agents or signaling molecules.

Example 10 below demonstrates this aspect of the invention. Specifically, table 61 demonstrates that both MEK and the NADPH oxidase inhibitors can limit bacterial replication (infection of IFN-γ-primed macrophages by S. typhimurium triggers a MEK kinase). This is an example of how bacterial survival can be impacted by changing host cell signaling molecules.

In still another aspect of the invention, compounds are presented that inhibit stromal derived factor-I (SDF-1) induced chemotaxis of T cells. Compounds are also presented which decrease expression of SDF-1 receptor. Such compounds also may act as an antagonist or inhibitor of CXCR-4. In one aspect the invention provides a cationic peptide that is an antagonist of CXCR-4. In another aspect the invention provides a method of identifying a cationic peptide that is an antagonist of CXCR-4. The method includes contacting T cells with SDF-1 in the presence of absence of a test peptide and measuring chemotaxis. A decrease in chemotaxis in the presence of the test peptide is then indicative of a peptide that is an antagonist of CXCR-4. Such compounds and methods are useful in therapeutic applications in HIV patients. These types of compounds and the utility thereof is demonstrated, for example, in Example 11 (see also Tables 62, 63). In that example, cationic peptides are shown to inhibit cell migration and therefore antiviral activity.

In one embodiment, the invention provides an isolated cationic peptides having an amino acid sequence of the general formula (Formula A): X₁X₂X₃IX₄PX₄IPX₅X₂X₁ (SEQ ID NO: 4), wherein X₁ is one or two of R, L or K, X₂ is one of C, S or A, X₃ is one of R or P, X₄ is one of A or V and X₅ is one of V or W. Examples of the peptides of the invention include, but are not limited to: LLCRIVPVIPWCK (SEQ ID NO: 5), LRCPIAPVIPVCKK (SEQ ID NO: 6), KSRIVPAIPVSLL (SEQ ID NO: 7), KKSPIAPAIPWSR (SEQ ID NO: 8), RRARIVPAIPVARR (SEQ ID NO: 9) and LSRIAPAIPWAKL (SEQ ID NO: 10).

In another embodiment, the invention provides an isolated linear cationic peptide having an amino acid sequence of the general formula (Formula B): X₁LX₂X₃KX₄X₂X₅X₃PX₃X₁ (SEQ ID NO: 11), wherein X₁ is one or two of D, E, S, T or N, X₂ is one or two of P, G or D, X₃ is one of G, A, V, L, I or Y, X₄ is one of R, K or H and X₅ is one of S, T, C, M or R. Examples of the peptides of the invention include, but are not limited to: DLPAKRGSAPGST (SEQ ID NO: 12), SELPGLKHPCVPGS (SEQ ID NO: 13), TTLGPVKRDSIPGE (SEQ ID NO: 14), SLPIKHDRLPATS (SEQ ID NO: 15), ELPLKRGRVPVE (SEQ ID NO: 16) and NLPDLKKPRVPATS (SEQ ID NO: 17).

In another embodiment, the invention provides an isolated linear cationic peptide having an amino acid sequence of the general formula (Formula C): X₁X₂X₃X₄WX₄WX₄X₅K (SEQ ID NO: 18) (this formula includes CP12a and CP12d), wherein X₁ is one to four chosen from A, P or R, X₂ is one or two aromatic amino acids (F, Y and W), X₃ is one of P or K, X₄ is one, two or none chosen from A, P, Y or W and X₅ is one to three chosen from R or P. Examples of the peptides of the invention include, but are not limited to: RPRYPWWPWWPYRPRK (SEQ ID NO: 19), RRAWWKAWWARRK (SEQ ID NO: 20), RAPYWPWAWARPRK (SEQ ID NO: 21), RPAWKYWWPWPWPRRK (SEQ ID NO: 22), RAAFKWAWAWWRRK (SEQ ID NO: 23) and RRRWKWAWPRRK (SEQ ID NO: 24).

In another embodiment, the invention provides an isolated hexadecameric cationic peptide having an amino acid sequence of the general formula (Formula D): X₁X₂X₃X₄X₁VX₃X₄RGX₄X₃X₄X₁X₃X₁ (SEQ ID NO: 25) wherein X₁ is one or two of R or K, X₂ is a polar or charged amino acid (S, T, M, N, Q, D, E, K, R and H), X₃ is C, S, M, D or A and X₄ is F, I, V, M or R. Examples of the peptides of the invention include, but are not limited to: RRMCIKVCVRGVCRRKCRK (SEQ ID NO: 26), KRSCFKVSMRGVSRRRCK (SEQ ID NO: 27), KKDAIKKVDIRGMDMRRAR (SEQ ID NO: 28), RKMVKVDVRGIMIRKDRR (SEQ ID NO: 29), KQCVKVAMRGMALRRCK (SEQ ID NO: 30) and RREAIRRVAMRGRDMKRMRR (SEQ ID NO: 31).

In still another embodiment, the invention provides an isolated hexadecameric cationic peptide having an amino acid sequence of the general formula (Formula E): X₁X₂X₃X₄X₁VX₅X₄RGX₄X₅X₄X₁X₃X₁ (SEQ ID NO: 32), wherein X₁ is one or two of R or K, X₂ is a polar or charged amino acid (S, T, M, N, Q, D, E, K, R and H), X₃ is one of C, S, M, D or A, X₄ is one of F, I, V, M or R and X₅ is one of A, I, S, M, D or R. Examples of the peptides of the invention include, but are not limited to: RTCVKRVAMRGIIRKRCR (SEQ ID NO: 33), KKQMMKRVDVRGISVKRKR (SEQ ID NO: 34), KESIKVIIRGMMVRMKK (SEQ ID NO: 35), RRDCRRVMVRGIDIKAK (SEQ ID NO: 36), KRTAIKKVSRRGMSVKARR (SEQ ID NO: 37) and RHClRRVSMRGIIMRRCK (SEQ ID NO: 38).

In another embodiment, the invention provides an isolated longer cationic peptide having an amino acid sequence of the general formula (Formula F): KX₁KX₂FX₂KMLMX₂ALKKX₃ (SEQ ID NO: 39), wherein X₁ is a polar amino acid (C, S, T, M, N and Q); X₂ is one of A, L, S or K and X₃ is 1-17 amino acids chosen from G, A, V, L, I, P, F, S, T, K and H. Examples of the peptides of the invention include, but are not limited to: KCKLFKKMLMLALKKVLTTGLPALKLTK (SEQ ID NO: 40), KSKSFLKMLMKALKKVLTTGLPALIS (SEQ ID NO: 41), KTKKFAKMLMMALKKVVSTAKPLAILS (SEQ ID NO: 42), KMKSFAKMLMLALKKVLKVLTTALTLKAGLPS (SEQ ID NO: 43), KNKAFAKMLMKALKKVTTAAKPLTG (SEQ ID NO: 44) and KQKLFAKMLMSALKKKTLVTTPLAGK (SEQ ID NO: 45).

In yet another embodiment, the invention provides an isolated longer cationic peptide having an amino acid sequence of the general formula (Formula G): KWKX₂X₁X₁X₂X₂X₁X₂X₂X₁X₁X₂X₂₁FHTALKPISS (SEQ ID NO: 46), wherein X₁ is a hydrophobic amino acid and X₂ is a hydrophilic amino acid. Examples of the peptides of the invention include, but are not limited to: KWKSFLRTFKSPVRTIFHTALKPISS (SEQ ID NO: 47), KWKSYAHTIMSPVRLIFHTALKPISS (SEQ ID NO: 48), KWKRGAHRFMKFLSTIFHTALKPISS (SEQ ID NO: 49), KWKKWAHSPRKVLTRIFHTALKPISS (SEQ ID NO: 50), KWKSLVMMFKKPARRIFHTALKPISS (SEQ ID NO: 51) and KWKHALMKAHMLWHMIFHTALKPISS (SEQ ID NO: 52).

In still another embodiment, the invention provides an isolated cationic peptide having an amino acid sequence of the formula: KWKSFLRTFKSPVRTVFHTALKPISS (SEQ ID NO: 53) or KWKSYAHTIMSPVRLVFHTALKPISS (SEQ ID NO: 54).

The term “isolated” as used herein refers to a peptide that is substantially free of other proteins, lipids, and nucleic acids (e.g., cellular components with which an in vivo-produced peptide would naturally be associated). Preferably, the peptide is at least 70%, 80%, or most preferably 90% pure by weight.

The invention also includes analogs, derivatives, conservative variations, and cationic peptide variants of the enumerated polypeptides, provided that the analog, derivative, conservative variation, or variant has a detectable activity in which it enhances innate immunity or has anti-inflammatory activity. It is not necessary that the analog, derivative, variation, or variant have activity identical to the activity of the peptide from which the analog, derivative, conservative variation, or variant is derived.

A cationic peptide “variant” is an peptide that is an altered form of a referenced cationic peptide. For example, the term “variant” includes a cationic peptide in which at least one amino acid of a reference peptide is substituted in an expression library. The term “reference” peptide means any of the cationic peptides of the invention (e.g., as defined in the above formulas), from which a variant, derivative, analog, or conservative variation is derived. Included within the term “derivative” is a hybrid peptide that includes at least a portion of each of two cationic peptides (e.g., 30-80% of each of two cationic peptides). Also included are peptides in which one or more amino acids are deleted from the sequence of a peptide enumerated herein, provided that the derivative has activity in which it enhances innate immunity or has anti-inflammatory activity. This can lead to the development of a smaller active molecule which would also have utility. For example, amino or carboxy terminal amino acids which may not be required for enhancing innate immunity or anti-inflammatory activity of a peptide can be removed. Likewise, additional derivatives can be produced by adding one or a few (e.g., less than 5) amino acids to a cationic peptide without completely inhibiting the activity of the peptide. In addition, C-terminal derivatives, e.g., C-terminal methyl esters, and N-terminal derivatives can be produced and are encompassed by the invention. Peptides of the invention include any analog, homolog, mutant, isomer or derivative of the peptides disclosed in the present invention, so long as the bioactivity as described herein remains. Also included is the reverse sequence of a peptide encompassed by the general formulas set forth above. Additionally, an amino acid of “D” configuration may be substituted with an amino acid of “L” configuration and vice versa. Alternatively the peptide may be cyclized chemically or by the addition of two or more cysteine residues within the sequence and oxidation to form disulphide bonds.

The invention also includes peptides that are conservative variations of those peptides exemplified herein. The term “conservative variation” as used herein denotes a polypeptide in which at least one amino acid is replaced by another, biologically similar residue. Examples of conservative variations include the substitution of one hydrophobic residue, such as isoleucine, valine, leucine, alanine, cysteine, glycine, phenylalanine, proline, tryptophan, tyrosine, norleucine or methionine for another, or the substitution of one polar residue for another, such as the substitution of arginine for lysine, glutamic for aspartic acid, or glutamine for asparagine, and the like. Neutral hydrophilic amino acids that can be substituted for one another include asparagine, glutamine, serine and threonine. The term “conservative variation” also encompasses a peptide having a substituted amino acid in place of an unsubstituted parent amino acid. Such substituted amino acids may include amino acids that have been methylated or amidated. Other substitutions will be known to those of skill in the art. In one aspect, antibodies raised to a substituted polypeptide will also specifically bind the unsubstituted polypeptide.

Peptides of the invention can be synthesized by commonly used methods such as those that include t-BOC or FMOC protection of alpha-amino groups. Both methods involve stepwise synthesis in which a single amino acid is added at each step starting from the C-terminus of the peptide (See, Coligan, et al., Current Protocols in Immunology, Wiley Interscience, 1991, Unit 9). Peptides of the invention can also be synthesized by the well known solid phase peptide synthesis methods such as those described by Merrifield, J. Am. Chem. Soc., 85:2149, 1962) and Stewart and Young, Solid Phase Peptides Synthesis, Freeman, San Francisco, 1969, pp.27-62) using a copoly(styrene-divinylbenzene) containing 0.1-1.0 mMol amines/g polymer. On completion of chemical synthesis, the peptides can be deprotected and cleaved from the polymer by treatment with liquid HF-10% anisole for about ¼-1 hours at 0° C. After evaporation of the reagents, the peptides are extracted from the polymer with a 1% acetic acid solution, which is then lyophilized to yield the crude material. The peptides can be purified by such techniques as gel filtration on Sephadex G-15 using 5% acetic acid as a solvent. Lyophilization of appropriate fractions of the column eluate yield homogeneous peptide, which can then be characterized by standard techniques such as amino acid analysis, thin layer chromatography, high performance liquid chromatography, ultraviolet absorption spectroscopy, molar rotation, or measuring solubility. If desired, the peptides can be quantitated by the solid phase Edman degradation.

The invention also includes isolated nucleic acids (e.g., DNA, cDNA, or RNA) encoding the peptides of the invention. Included are nucleic acids that encode analogs, mutants, conservative variations, and variants of the peptides described herein. The term “isolated” as used herein refers to a nucleic acid that is substantially free of proteins, lipids, and other nucleic acids with which an in vivo-produced nucleic acids naturally associated. Preferably, the nucleic acid is at least 70%, 80%, or preferably 90% pure by weight, and conventional methods for synthesizing nucleic acids in vitro can be used in lieu of in vivo methods. As used herein, “nucleic acid” refers to a polymer of deoxyribo-nucleotides or ribonucleotides, in the form of a separate fragment or as a component of a larger genetic construct (e.g., by operably linking a promoter to a nucleic acid encoding a peptide of the invention). Numerous genetic constructs (e.g., plasmids and other expression vectors) are known in the art and can be used to produce the peptides of the invention in cell-free systems or prokaryotic or eukaryotic (e.g., yeast, insect, or mammalian) cells. By taking into account the degeneracy of the genetic code, one of ordinary skill in the art can readily synthesize nucleic acids encoding the polypeptides of the invention. The nucleic acids of the invention can readily be used in conventional molecular biology methods to produce the peptides of the invention.

DNA encoding the cationic peptides of the invention can be inserted into an “expression vector.” The term “expression vector” refers to a genetic construct such as a plasmid, virus or other vehicle known in the art that can be engineered to contain a nucleic acid encoding a polypeptide of the invention. Such expression vectors are preferably plasmids that contain a promoter sequence that facilitates transcription of the inserted genetic sequence in a host cell. The expression vector typically contains an origin of replication, and a promoter, as well as polynucleotides that allow phenotypic selection of the transformed cells (e.g., an antibiotic resistance polynucleotide). Various promoters, including inducible and constitutive promoters, can be utilized in the invention. Typically, the expression vector contains a replicon site and control sequences that are derived from a species compatible with the host cell.

Transformation or transfection of a recipient with a nucleic acid of the invention can be carried out using conventional techniques well known to those skilled in the art. For example, where the host cell is E. coli, competent cells that are capable of DNA uptake can be prepared using the CaCl₂, MgCl₂ or RbCl methods known in the art. Alternatively, physical means, such as electroporation or microinjection can be used. Electroporation allows transfer of a nucleic acid into a cell by high voltage electric impulse. Additionally, nucleic acids can be introduced into host cells by protoplast fusion, using methods well known in the art. Suitable methods for transforming eukaryotic cells, such as electroporation and lipofection, also are known.

“Host cells” or “Recipient cells” encompassed by of the invention are any cells in which the nucleic acids of the invention can be used to express the polypeptides of the invention. The term also includes any progeny of a recipient or host cell. Preferred recipient or host cells of the invention include E. coli, S. aureus and P. aeruginosa, although other Gram-negative and Gram-positive bacterial, fungal and mammalian cells and organisms known in the art can be utilized as long as the expression vectors contain an origin of replication to permit expression in the host.

The cationic peptide polynucleotide sequence used according to the method of the invention can be isolated from an organism or synthesized in the laboratory. Specific DNA sequences encoding the cationic peptide of interest can be obtained by: 1) isolation of a double-stranded DNA sequence from the genomic DNA; 2) chemical manufacture of a DNA sequence to provide the necessary codons for the cationic peptide of interest; and 3) in vitro synthesis of a double-stranded DNA sequence by reverse transcription of mRNA isolated from a donor cell. In the latter case, a double-stranded DNA complement of mRNA is eventually formed which is generally referred to as cDNA.

The synthesis of DNA sequences is frequently the method of choice when the entire sequence of amino acid residues of the desired peptide product is known. In the present invention, the synthesis of a DNA sequence has the advantage of allowing the incorporation of codons which are more likely to be recognized by a bacterial host, thereby permitting high level expression without difficulties in translation. In addition, virtually any peptide can be synthesized, including those encoding natural cationic peptides, variants of the same, or synthetic peptides.

When the entire sequence of the desired peptide is not known, the direct synthesis of DNA sequences is not possible and the method of choice is the formation of cDNA sequences. Among the standard procedures for isolating cDNA sequences of interest is the formation of plasmid or phage containing cDNA libraries which are derived from reverse transcription of mRNA which is abundant in donor cells that have a high level of genetic expression. When used in combination with polymerase chain reaction technology, even rare expression products can be cloned. In those cases where significant portions of the amino acid sequence of the cationic peptide are known, the production of labeled single or double-stranded DNA or RNA probe sequences duplicating a sequence putatively present in the target cDNA may be employed in DNA/DNA hybridization procedures which are carried out on cloned copies of the cDNA which have been denatured into a single stranded form (Jay, et al., Nuc. Acid Res., 11:2325, 1983).

The peptide of the invention can be administered parenterally by injection or by gradual infusion over time. Preferably the peptide is administered in a therapeutically effective amount to enhance or to stimulate an innate immune response. Innate immunity has been described herein, however examples of indicators of stimulation of innate immunity include but are not limited to monocyte activation, proliferation, differentiation or MAP kinase pathway activation.

The peptide can be administered intravenously, intraperitoneally, intramuscularly, subcutaneously, intracavity, or transdermally. Preferred methods for delivery of the peptide include orally, by encapsulation in microspheres or proteinoids, by aerosol delivery to the lungs, or transdermally by iontophoresis or transdermal electroporation. Other methods of administration will be known to those skilled in the art.

Preparations for parenteral administration of a peptide of the invention include sterile aqueous or non-aqueous solutions, suspensions, and emulsions. Examples of non-aqueous solvents are propylene glycol, polyethylene glycol, vegetable oils such as olive oil, and injectable organic esters such as ethyl oleate. Aqueous carriers include water, alcoholic/aqueous solutions, emulsions or suspensions, including saline and buffered media Parenteral vehicles include sodium chloride solution, Ringer's dextrose, dextrose and sodium chloride, lactated Ringer's, or fixed oils. Intravenous vehicles include fluid and nutrient replenishers, electrolyte replenishers (such as those based on Ringer's dextrose), and the like. Preservatives and other additives may also be present such as, for example, antimicrobials, anti-oxidants, chelating agents, and inert gases and the like.

In one embodiment, the invention provides a method for synergistic therapy. For example, peptides as described herein can be used in synergistic combination with sub-inhibitory concentrations of antibiotics. Examples of particular classes of antibiotics useful for synergistic therapy with the peptides of the invention include aminoglycosides (e.g., tobramycin), penicillins (e.g., piperacillin), cephalosporins (e.g., ceftazidime), fluoroquinolones (e.g., ciprofloxacin), carbapenems (e.g., imipenem), tetracyclines and macrolides (e.g., erythromycin and clarithromycin). Further to the antibiotics listed above, typical antibiotics include aminoglycosides (amikacin, gentamicin, kanamycin, netilmicin, tobramycin, streptomycin, azithromycin, clarithromycin, erythromycin, erythromycin estolate/ethylsuccinate/gluceptate/lactobionate/stearate), beta-lactams such as penicillins (e.g., penicillin G, penicillin V, methicillin, nafcillin, oxacillin, cloxacillin, dicloxacillin, ampicillin, amoxicillin, ticarcillin, carbenicillin, mezlocillin, azlocillin and piperacillin), or cephalosporins (e.g., cephalothin, cefazolin, cefaclor, cefamandole, cefoxitin, cefuroxime, cefonicid, ceftmetazole, cefotetan, cefprozil, loracarbef, cefetamet, cefoperazone, cefotaxime, ceftizoxime, ceftriaxone, ceftazidime, cefepime, cefixime, cefpodoxime, and cefsulodin). Other classes of antibiotics include carbapenems (e.g., imipenem), monobactams (e.g., aztreonam), quinolones (e.g., fleroxacin, nalidixic acid, norfloxacin, ciprofloxacin, ofloxacin, enoxacin, lomefloxacin and cinoxacin), tetracyclines (e.g., doxycycline, minocycline, tetracycline), and glycopeptides (e.g., vancomycin, teicoplanin), for example. Other antibiotics include chloramphenicol, clindamycin, trimethoprim, sulfamethoxazole, nitrofurantoin, rifampin, mupirocin and the cationic peptides.

The efficacy of peptides was evaluated therapeutically alone and in combination with sub-optimal concentrations of antibiotics in models of infection. S. aureus is an important Gram positive pathogen and a leading cause of antibiotic resistant infections. Briefly, peptides were tested for therapeutic efficacy in the S. aureus infection model by injecting them alone and in combination with sub-optimal doses of antibiotics 6 hours after the onset of infection. This would simulate the circumstances of antibiotic resistance developing during an infection, such that the MIC of the resistant bacterium was too high to permit successful therapy (i.e the antibiotic dose applied was sub-optimal). It was demonstrated that the combination of antibiotic and peptide resulted in improved efficacy and suggests the potential for combination therapy (see Example 12).

The invention will now be described in greater detail by reference to the following non-limiting examples. While the invention has been described in detail with reference to certain preferred embodiments thereof, it will be understood that modifications and variations are within the spirit and scope of that which is described and claimed.

EXAMPLE 1 Anti-Sepsis/Anti-Inflammatory Activity

Polynucleotide arrays were utilized to determine the effect of cationic peptides on the transcriptional response of epithelial cells. The A549 human epithelial cell line was maintained in DMEM (Gibco) supplemented with 10% fetal bovine serum (FBS, Medicorp). The A549 cells were plated in 100 mm tissue culture dishes at 2.5×10⁶ cells/dish, cultured overnight and then incubated with 100 ng/ml E. coli O111:B4 LPS (Sigma), without (control) or with 50 μg/ml peptide or medium alone for 4 h. After stimulation, the cells were washed once with diethyl pyrocarbonate-treated phosphate buffered saline (PBS), and detached from the dish using a cell scraper. Total RNA was isolated using RNAqueous (Ambion, Austin, Tex.). The RNA pellet was resuspended in RNase-free water containing Superase-In (RNase inhibitor; Ambion). DNA contamination was removed with DNA-free kit, Ambion). The quality of the RNA was assessed by gel electrophoresis on a 1% agarose gel.

The polynucleotide arrays used were the Human Operon arrays (identification number for the genome is PRHU04-S1), which consist of about 14,000 human oligos spotted in duplicate. Probes were prepared from 10 μg of total RNA and labeled with Cy3 or Cy5 labeled dUTP. The probes were purified and hybridized to printed glass slides overnight at 42° C. and washed. After washing, the image was captured using a Perkin Elmer array scanner. The image processing software (Imapolynucleotide 5.0, Marina Del Rey, Calif.) determines the spot mean intensity, median intensities, and background intensities. A “homemade” program was used to remove background. The program calculates the bottom 10% intensity for each subgrid and subtracts this for each grid. Analysis was performed with Genespring software (Redwood City, Calif.). The intensities for each spot were normalized by taking the median spot intensity value from the population of spot values within a slide and comparing this value to the values of all slides in the experiment. The relative changes seen with cells treated with peptide compared to control cells can be found in Tables 1 and 2. These tables 2 reflect only those polynucleotides that demonstrated significant changes in expression of the 14,000 polynucleotides that were tested for altered expression. The data indicate that the peptides have a widespread ability to reduce the expression of polynucleotides that were induced by LPS.

In Table 1, the peptide, SEQ ID NO: 27 is shown to potently reduce the expression of many of the polynucleotides up-regulated by E. coli O111:B4 LPS as studied by polynucleotide microarrays. Peptide (50 μg/ml) and LPS (0.1 μg/ml) or LPS alone was incubated with the A549 cells for 4 h and the RNA was isolated. Five μg total RNA was used to make Cy3/Cy5 labeled cDNA probes and hybridized onto Human Operon arrays (PRHU04). The intensity of unstimulated cells is shown in the third column of Table 1. The “Ratio: LPS/control” column refers to the intensity of polynucleotide expression in LPS simulated cells divided by in the intensity of unstimulated cells. The “Ratio: LPS+ID 27/control” column refers to the intensity of polynucleotide expression in cells stimulated with LPS and peptide divided by unstimulated cells.

TABLE 1 Reduction, by peptide SEQ ID 27, of A549 human epithelial cell polynucleotide expression up-regulated by E. coli O111:B4 LPS Accession Polynucleotide Control: Media Ratio: Ratio: LPS + ID Number^(a) Gene Function only Intensity LPS/control 27/control AL031983 Unknown 0.032 302.8 5.1 L04510 ADP- 0.655 213.6 1.4 ribosylation factor D87451 ring finger 3.896 183.7 2.1 protein 10 AK000869 hypothetical 0.138 120.1 2.3 protein U78166 Ric-like 0.051 91.7 0.2 expressed in neurons AJ001403 mucin 5 0.203 53.4 15.9 subtype B tracheobronchial AB040057 serine/threonine 0.95 44.3 15.8 protein kinase MASK Z99756 Unknown 0.141 35.9 14.0 L42243 interferon 0.163 27.6 5.2 receptor 2 NM_016216 RNA lariat 6.151 22.3 10.9 debranching enzyme AK001589 hypothetical 0.646 19.2 1.3 protein AL137376 Unknown 1.881 17.3 0.6 AB007856 FEM-1-like 2.627 15.7 0.6 death receptor binding protein AB007854 growth arrest- 0.845 14.8 2.2 specific 7 AK000353 cytosolic 0.453 13.5 1.0 ovarian carcinoma antigen 1 D14539 myeloid/lymphoid 2.033 11.6 3.1 or mixed- lineage leukemia translocated to 1 X76785 integration site 0.728 11.6 1.9 for Epstein-Barr virus M54915 pim-1 1.404 11.4 0.6 oncogene NM_006092 caspase 0.369 11.0 0.5 recruitment domain 4 J03925 integrin_alpha M 0.272 9.9 4.2 NM_001663 ADP- 0.439 9.7 1.7 ribosylation factor 6 M23379 RAS p21 0.567 9.3 2.8 protein activator K02581 thymidine 3.099 8.6 3.5 kinase 1 soluble U94831 transmembrane 3.265 7.1 1.5 9 superfamily member 1 X70394 zinc finger 1.463 6.9 1.7 protein 146 AL137614 hypothetical 0.705 6.8 1.0 protein U43083 guanine 0.841 6.6 1.6 nucleotide binding protein AL137648 DKFZp434J181 1.276 6.5 0.8 3 protein AF085692 ATP-binding 3.175 6.5 2.4 cassette sub- family C (CFTR/MRP) member 3 AK001239 hypothetical 2.204 6.4 1.3 protein FLJ10377 NM_001679 ATPase 2.402 6.3 0.9 Na+/K+ transporting beta 3 polypeptide L24804 unactive 3.403 6.1 1.1 progesterone receptor U15932 dual specificity 0.854 6.1 2.1 phosphatase 5 M36067 ligase I DNA_(—) 1.354 6.1 2.2 ATP-dependent AL161951 Unknown 0.728 5.8 1.9 M59820 colony 0.38 5.7 2.0 stimulating factor 3 receptor AL050290 spermidine/ 2.724 5.6 1.4 spermine N1- acetyltransferase NM_002291 laminin_beta 1 1.278 5.6 1.8 X06614 retinoic acid 1.924 5.5 0.8 receptor_alpha AB007896 putative L-type 0.94 5.3 1.8 neutral amino acid transporter AL050333 DKFZP564B11 1.272 5.3 0.6 6 protein AK001093 hypothetical 1.729 5.3 2.0 protein NM_016406 hypothetical 1.314 5.2 1.2 protein M86546 pre-B-cell 1.113 5.2 2.2 leukemia tran- scription factor 1 X56777 zona pellucida 1.414 5.0 1.4 glycoprotein 3A NM_013400 replication 1.241 4.9 2.0 initiation region protein NM_002309 leukemia 1.286 4.8 1.9 inhibitory factor NM_001940 dentatorubral- 2.034 4.7 1.2 pallidoluysian atrophy U91316 cytosolic acyl 2.043 4.7 1.4 coenzyme A thioester hydrolase X76104 death- 1.118 4.6 1.8 associated protein kinase 1 AF131838 Unknown 1.879 4.6 1.4 AL050348 Unknown 8.502 4.4 1.7 D42085 KIAA0095 gene 1.323 4.4 1.2 product X92896 Unknown 1.675 4.3 1.5 U26648 syntaxin 5A 1.59 4.3 1.4 X85750 monocyte to 1.01 4.3 1.1 macrophage differentiation- associated D14043 CD 164 1.683 4.2 1.0 antigen_(—) sialomucin J04513 fibroblast 1.281 4.0 0.9 growth factor 2 U19796 melanoma- 1.618 4.0 0.6 associated antigen AK000087 hypothetical 1.459 3.9 1.0 protein AK001569 hypothetical 1.508 3.9 1.2 protein AF189009 ubiquilin 2 1.448 3.8 1.3 U60205 sterol-C4- 1.569 3.7 0.8 methyl oxidase- like AK000562 hypothetical 1.166 3.7 0.6 protein AL096739 Unknown 3.66 3.7 0.5 AK000366 hypothetical 15.192 3.5 1.0 protein NM_006325 RAN member 1.242 3.5 1.4 RAS oncogene family X51688 cyclin A2 1.772 3.3 1.0 U34252 aldehyde 1.264 3.3 1.2 dehydrogenase 9 NM_013241 FH1/FH2 1.264 3.3 0.6 domain- containing protein AF112219 esterase 1.839 3.3 1.1 D/formylglutathione hydrolase NM_016237 anaphase- 2.71 3.2 0.9 promoting complex subunit 5 AB014569 KIAA0669 gene 2.762 3.2 0.2 product AF151047 hypothetical 3.062 3.1 1.0 protein X92972 protein 2.615 3.1 1.1 phosphatase 6 catalytic subunit AF035309 proteasome 5.628 3.1 1.3 26S subunit ATPase 5 U52960 SRB7 homolog 1.391 3.1 0.8 J04058 electron- 3.265 3.1 1.2 transfer- flavoprotein alpha polypeptide M57230 interleukin 6 signal 0.793 3.1 1.0 transducer U78027 galactosidase_(—) 3.519 3.1 1.1 alpha AK000264 Unknown 2.533 3.0 0.6 X80692 mitogen- 2.463 2.9 1.3 activated protein kinase 6 L25931 lamin B 2.186 2.7 0.7 receptor X13334 CD14 antigen 0.393 2.5 1.1 M32315 tumor necrosis 0.639 2.4 0.4 factor receptor superfamily member 1B NM_004862 LPS-induced 6.077 2.3 1.1 TNF-alpha factor AL050337 interferon 2.064 2.1 1.0 gamma receptor 1 ^(a)All Accession Numbers in Table 1 through Table 64 refer to GenBank Accession Numbers.

In Table 2, the cationic peptides at a concentration of 50 μg/ml were shown to potently reduce the expression of many of the polynucleotides up-regulated by 100 ng/ml E. coli O111:B4 LPS as studied by polynucleotide microarrays. Peptide and LPS or LPS alone was incubated with the A549 cells for 4 h and the RNA was isolated. 5 μg total RNA was used to make Cy3/Cy5 labeled cDNA probes and hybridized onto Human Operon arrays (PRHU04). The intensity of unstimulated cells is shown in the third column of Table 2. The “Ratio: LPS/control” column refers to the intensity of polynucleotide expression in LPS-simulated cells divided by in the intensity of unstimulated cells. The other columns refer to the intensity of polynucleotide expression in cells stimulated with LPS and peptide divided by unstimulated cells.

TABLE 2 Human A549 Epithelial Cell Polynucleotide Expression up-regulated by E.coli O111:B4 LPS and reduced by Cationic Peptides Control: Ratio: Ratio: Ratio: Accession Media only Ratio: LPS + ID 27/ LPS + ID 16/ LPS + ID 22/ Number Gene Intensity LPS/control control control control AL031983 Unknown 0.03 302.8 5.06 6.91 0.31 L04510 ADP- 0.66 213.6 1.4 2.44 3.79 ribosylation factor D87451 ring finger 3.90 183.7 2.1 3.68 4.28 protein AK000869 hypothetical 0.14 120.1 2.34 2.57 2.58 protein U78166 Ric like 0.05 91.7 0.20 16.88 21.37 X03066 MHC class II 0.06 36.5 4.90 12.13 0.98 DO beta AK001904 hypothetical 0.03 32.8 5.93 0.37 0.37 protein AB037722 Unknown 0.03 21.4 0.30 0.30 2.36 AK001589 hypothetical 0.65 19.2 1.26 0.02 0.43 protein AL137376 Unknown 1.88 17.3 0.64 1.30 1.35 L19185 thioredoxin- 0.06 16.3 0.18 2.15 0.18 dependent peroxide reductase 1 J05068 transcobalaminl 0.04 15.9 1.78 4.34 0.83 AB007856 FEM-1-like 2.63 15.7 0.62 3.38 0.96 death receptor binding protein AK000353 cytosolic 0.45 13.5 1.02 1.73 2.33 ovarian carcinoma ag 1 X16940 smooth muscle 0.21 11.8 3.24 0.05 2.26 enteric actin _(γ)2 M54915 pim-1 oncogene 1.40 11.4 0.63 1.25 1.83 AL122111 hypothetical 0.37 10.9 0.21 1.35 0.03 protein M95678 phospholipase 0.22 7.2 2.38 0.05 1.33 C beta 2 AK001239 hypothetical 2.20 6.4 1.27 1.89 2.25 protein AC004849 Unknown 0.14 6.3 0.07 2.70 0.07 X06614 retinoic acid 1.92 5.5 0.77 1.43 1.03 receptor_alpha AB007896 putative L-type 0.94 5.3 1.82 2.15 2.41 neutral amino acid transporter AB010894 BAl1-associated 0.69 5.0 1.38 1.03 1.80 protein U52522 partner of RAC1 1.98 2.9 1.35 0.48 1.38 AK001440 hypothetical 1.02 2.7 0.43 1.20 0.01 protein NM_001148 ankyrin 2_(—) 0.26 2.5 0.82 0.04 0.66 neuronal X07173 inter-alpha 0.33 2.2 0.44 0.03 0.51 inhibitor H2 AF095687 brain and 0.39 2.1 0.48 0.03 0.98 nasopharyngeal carcinoma susceptibility protein NM_016382 NK cell 0.27 2.1 0.81 0.59 0.04 activation inducing ligand NAIL AB023198 KIAA0981 0.39 2.0 0.43 0.81 0.92 protein

EXAMPLE 2 Neutralization of the Stimulation of Immune Cells

The ability of compounds to neutralize the stimulation of immune cells by both Gram-negative and Gram-positive bacterial products was tested. Bacterial products stimulate cells of the immune system to produce inflammatory cytokines and when unchecked this can lead to sepsis. Initial experiments utilized the murine macrophage cell line RAW 264.7, which was obtained from the American Type Culture Collection, (Manassas, Va.), the human epithelial cell line, A549, and primary macrophages derived from the bone marrow of BALB/c mice (Charles River Laboratories, Wilmington, Mass.). The cells from mouse bone marrow were cultured in 150-mm plates in Dulbecco's modified Eagle medium (DMEM; Life Technologies, Burlington, ON) supplemented with 20% FBS (Sigma Chemical Co, St. Louis, Mo.) and 20% L cell-conditioned medium as a source of M-CSF. Once macrophages were 60-80% confluent, they were deprived of L cell-conditioned medium for 14-16 h to render the cells quiescent and then were subjected to treatments with 100 ng/ml LPS or 100 ng/ml LPS+20 μg/ml peptide for 24 hours. The release of cytokines into the culture supernatant was determined by ELISA (R&D Systems, Minneapolis, Minn.). The cell lines, RAW 264.7 and A549, were maintained in DMEM supplemented with 10% fetal calf serum. RAW 264.7 cells were seeded in 24 well plates at a density of 10⁶ cells per well in DMEM and A549 cells were seeded in 24 well plates at a density of 1 cells per well in DMEM and both were incubated at 37° C. in 5% CO₂ overnight. DMEM was aspirated from cells grown overnight and replaced with fresh medium. In some experiments, blood from volunteer human donors was collected (according to procedures accepted by UBC Clinical Research Ethics Board, certificate C00-0537) by venipuncture into tubes (Becton Dickinson, Franklin Lakes, N.J.) containing 14.3 USP units heparin/ml blood. The blood was mixed with LPS with or without peptide in polypropylene tubes at 37° C. for 6 h. The samples were centrifuged for 5 min at 2000×g, the plasma was collected and then stored at −20° C. until being analyzed for IL-8 by ELISA (R&D Systems). In the experiments with cells, LPS or other bacterial products were incubated with the cells for 6-24 hr at 37° C. in 5% CO₂ . S. typhimurium LPS and E. coli 0111:B4 LPS were purchased from Sigma. Lipoteichoic acid (LTA) from S. aureus (Sigma) was resuspended in endotoxin free water (Sigma). The Limulus amoebocyte lysate assay (Sigma) was performed on LTA preparations to confirm that lots were not significantly contaminated by endotoxin. Endotoxin contamination was less than 1 ng/ml, a concentration that did not cause significant cytokine production in the RAW 264.7 cells. Non-capped lipoarabinomannan (AraLAM) was a gift from Dr. John T. Belisle of Colorado State University. The AraLAM from Mycobacterium was filter sterilized and the endotoxin contamination was found to be 3.75 ng per 1.0 mg of LAM as determined by Limulus Amebocyte assay. At the same time as LPS addition (or later where specifically described), cationic peptides were added at a range of concentrations. The supernatants were removed and tested for cytokine production by ELISA (R&D Systems). All assays were performed at least three times with similar results. To confirm the anti-sepsis activity in vivo, sepsis was induced by intraperitoneal injection of 2 or 3 μg of E. coli O111:B4 LPS in phosphate-buffered saline (PBS; pH 7.2) into galactosamine-sensitized 8- to 10-week-old female CD-1 or BALB/c mice. In experiments involving peptides, 200 μg in 100 μl of sterile water was injected at separate intraperitoneal sites within 10 min of LPS injection. In other experiments, CD-1 mice were injected with 400 μg E. coli O111:B4 LPS and 10 min later peptide (200 μg) was introduced by intraperitoneal injection. Survival was monitored for 48 hours post injection.

Hyperproduction of TNF-α has been classically linked to development of sepsis. The three types of LPS, LTA or AraLAM used in this example represented products released by both Gram-negative and Gram-positive bacteria. Peptide, SEQ ID NO: 1, was able to significantly reduce TNF-α production stimulated by S. typhimurium, B. cepacia, and E. coli O111:B4 LPS, with the former being affected to a somewhat lesser extent (Table 3). At concentrations as low as 1 μg/ml of peptide (0.25 nM) substantial reduction of TNF-α production was observed in the latter two cases. A different peptide, SEQ ID NO: 3 did not reduce LPS-induced production of TNF-α in RAW macrophage cells, demonstrating that this is not a uniform and predictable property of cationic peptides. Representative peptides from each Formula were also tested for their ability to affect TNF-α production stimulated by E. coli O111:B4 LPS (Table 4). The peptides had a varied ability to reduce TNF-α production although many of them lowered TNF-α by at least 60%.

At certain concentrations peptides SEQ ID NO: 1 and SEQ ID NO: 2, could also reduce the ability of bacterial products to stimulate the production of IL-8 by an epithelial cell line. LPS is a known potent stimulus of IL-8 production by epithelial cells. Peptides, at low concentrations (1-20 μg/ml), neutralized the IL-8 induction responses of epithelial cells to LPS (Table 5-7). Peptide SEQ ID 2 also inhibited LPS-induced production of IL-8 in whole human blood (Table 4). Conversely, high concentrations of peptide SEQ ID NO: 1 (50 to 100 μg/ml) actually resulted in increased levels of IL-8 (Table 5). This suggests that the peptides have different effects at different concentrations.

The effect of peptides on inflammatory stimuli was also demonstrated in primary murine cells, in that peptide SEQ ID NO: 1 significantly reduced TNF-α production (>90%) by bone marrow-derived macrophages from BALB/c mice that had been stimulated with 100 ng/ml E. coli 0111:B4 LPS (Table 8). These experiments were performed in the presence of serum, which contains LPS-binding protein (LBP), a protein that can mediate the rapid binding of LPS to CD14. Delayed addition of SEQ ID NO: 1 to the supernatants of macrophages one hour after stimulation with 100 ng/ml E. coli LPS still resulted in substantial reduction (70%) of TNF-α production (Table 9).

Consistent with the ability of SEQ ID NO: 1 to prevent LPS-induced production of TNF-α in vitro, certain peptides also protected mice against lethal shock induced by high concentrations of LPS. In some experiments, CD-1 mice were sensitized to LPS with a prior injection of galactosamine. Galactosamine-sensitized mice that were injected with 3 μg of E. coli 0111:B4 LPS were all killed within 4-6 hours. When 200 μg of SEQ ID NO: 1 was injected 15 min after the LPS, 50% of the mice survived (Table 10). In other experiments when a higher concentration of LPS was injected into BALB/c mice with no D-galactosamine, peptide protected 100% compared to the control group in which there was no survival (Table 13). Selected other peptides were also found to be protective in these models (Tables 11, 12).

Cationic peptides were also able to lower the stimulation of macrophages by Gram-positive bacterial products such as Mycobacterium non-capped lipoarabinomannan (AraLAM) and S. aureus LTA. For example, SEQ ID NO: 1 inhibited induction of TNF-α in RAW 264.7 cells by the Gram-positive bacterial products, LTA (Table 14) and to a lesser extent AraLAM (Table 15). Another peptide, SEQ ID NO: 2, was also found to reduce LTA-induced TNF-α production by RAW 264.7 cells. At a concentration of 1 μg/ml SEQ ID NO: 1 was able to substantially reduce (>75%) the induction of TNF-α production by 1 μg/ml S. aureus LTA. At 20 μg/ml SEQ ID NO: 1, there was >60% inhibition of AraLAM induced TNF-α. Polymyxin B (PMB) was included as a control to demonstrate that contaminating endotoxin was not a significant factor in the inhibition by SEQ ID NO: 1 of AraLAM induced TNF-α. These results demonstrate that cationic peptides can reduce the pro-inflammatory cytokine response of the immune system to bacterial products.

TABLE 3 Reduction by SEQ ID 1 of LPS induced TNF-α production in RAW 264.7 cells. RAW 264.7 mouse macrophage cells were stimulated with 100 ng/ml S. typhimurium LPS, 100 ng/ml B. cepacia LPS and 100 ng/ml E. coli 0111:B4 LPS in the presence of the indicated concentrations of SEQ ID 1 for 6 hr. The concentrations of TNF-α released into the culture supernatants were determined by ELISA. 100% represents the amount of TNF-α resulting from RAW 264.7 cells incubated with LPS alone for 6 hours (S. typhimurium LPS = 34.5 ± 3.2 ng/ml, B. cepacia LPS = 11.6 ± 2.9 ng/ml, and E. coli 0111:B4 LPS = 30.8 ± 2.4 ng/ml). Background levels of TNF-α production by the RAW 264.7 cells cultured with no stimuli for 6 hours resulted in TNF-α levels ranging from 0.037-0.192 ng/ml. The data is from duplicate samples and presented as the mean of three experiments + standard error. Amount of SEQ ID Inhibition of TNF-α (%)* 1 (μ/ml) B. cepacia LPS E. coli LPS S. typhimurium LPS 0.1  8.5 ± 2.9  0.0 ± 0.6  0.0 ± 0 1 23.0 ± 11.4 36.6 ± 7.5  9.8 ± 6.6 5 55.4 ± 8 65.0 ± 3.6 31.1 ± 7.0 10 63.1 ± 8 75.0 ± 3.4 37.4 ± 7.5 20 71.7 ± 5.8 81.0 ± 3.5 58.5 ± 10.5 50 86.7 ± 4.3 92.6 ± 2.5 73.1 ± 9.1

TABLE 4 Reduction by Cationic Peptides of E. coli LPS induced TNF-α production in RAW 264.7 cells. RAW 264.7 mouse macrophage cells were stimulated with 100 ng/ml E. coli 0111:B4 LPS in the presence of the indicated concentrations of cationic peptides for 6 h. The concentrations of TNF-α released into the culture supernatants were determined by ELISA. Background levels of TNF-α production by the RAW 264.7 cells cultured with no stimuli for 6 hours resulted in TNF-α levels ranging from 0.037-0.192 ng/ml. The data is from duplicate samples and presented as the mean of three experiments + standard deviation. Peptide (20 μ/ml) Inhibition of TNF-α (%) SEQ ID 5 65.6 ± 1.6 SEQ ID 6 59.8 ± 1.2 SEQ ID 7 50.6 ± 0.6 SEQ ID 8 39.3 ± 1.9 SEQ ID 9 58.7 ± 0.8 SEQ ID 10 55.5 ± 0.52 SEQ ID 12 52.1 ± 0.38 SEQ ID 13 62.4 ± 0.85 SEQ ID 14 50.8 ± 1.67 SEQ ID 15 69.4 ± 0.84 SEQ ID 16 37.5 ± 0.66 SEQ ID 17 28.3 ± 3.71 SEQ ID 19 69.9 ± 0.09 SEQ ID 20 66.1 ± 0.78 SEQ ID 21 67.8 ± 0.6 SEQ ID 22 73.3 ± 0.36 SEQ ID 23 83.6 ± 0.32 SEQ ID 24 60.5 ± 0.17 SEQ ID 26 54.9 ± 1.6 SEQ ID 27 51.1 ± 2.8 SEQ ID 28 56 ± 1.1 SEQ ID 29 58.9 ± 0.005 SEQ ID 31 60.3 ± 0.6 SEQ ID 33 62.1 ± 0.08 SEQ ID 34 53.3 ± 0.9 SEQ ID 35 60.7 ± 0.76 SEQ ID 36 63 ± 0.24 SEQ ID 37 58.9 ± 0.67 SEQ ID 38 54 ± 1 SEQ ID 40 75 ± 0.45 SEQ ID 41 86 ± 0.37 SEQ ID 42 80.5 ± 0.76 SEQ ID 43 88.2 ± 0.65 SEQ ID 44 44.9 ± 1.5 SEQ ID 45 44.7 ± 0.39 SEQ ID 47 36.9 ± 2.2 SEQ ID 48 64 ± 0.67 SEQ ID 49 86.9 ± 0.69 SEQ ID 53 46.5 ± 1.3 SEQ ID 54 64 ± 0.73

TABLE 5 Reduction by SEQ ID 1 of LPS induced IL-8 production in A549 cells. A549 cells were stimulated with increasing concentrations of SEQ ID 1 in the presence of LPS (100 ng/ml E. coli O111:B4) for 24 hours. The concentration of IL-8 in the culture supernatants was determined by ELISA. The background levels of IL-8 from cells alone was 0.172 ± 0.029 ng/ml. The data is presented as the mean of three experiments + standard error. SEQ ID 1 (μ/ml) Inhibition of IL-8 (%) 0.1   1 ± 0.3 1 32 ± 10 10 60 ± 9  20 47 ± 12 50 40 ± 13 100 0

TABLE 6 Reduction by SEQ ID 2 of E. coli LPS induced IL-8 production in A549 cells. Human A549 epithelial cells were stimulated with increasing concentrations of SEQ ID 2 in the presence of LPS (100 ng/ml E. coli O111:B4) for 24 hours. The concentration of IL-8 in the culture supernatants was determined by ELISA. The data is presented as the mean of three experiments + standard error. Concentration of Inhibition of SEQ ID 2 (μ/ml) IL-8 (%) 0.1  6.8 ± 9.6 1  12.8 ± 24.5 10  29.0 ± 26.0 50 39.8 ± 1.6 100 45.0 ± 3.5

TABLE 7 Reduction by SEQ ID 2 of E. coli LPS induced IL-8 in human blood. Whole human blood was stimulated with increasing concentrations of peptide and E.coli O111:B4 LPS for 4 hr. The human blood samples were centrifuged and the serum was removed and tested for IL-8 by ELISA. The data is presented as the average of 2 donors. SEQ ID 2 (μ/ml) IL-8 (pg/ml) 0 3205 10 1912 50 1458

TABLE 8 Reduction by SEQ ID 1 of E. coli LPS induced TNF-α production in murine bone marrow macrophages. BALB/c Mouse bone marrow-derived macrophages were cultured for either 6 h or 24 h with 100 ng/ml E. coli 0111:B4 LPS in the presence or absence of 20 μ/ml of peptide. The supernatant was collected and tested for levels of TNF-α by ELISA. The data represents the amount of TNF-α resulting from duplicate wells of bone marrow-derived macrophages incubated with LPS alone for 6 h (1.1 ± 0.09 ng/ml) or 24 h (1.7 ± 0.2 ng/ml). Background levels of TNF-α were 0.038 ± 0.008 ng/ml for 6 h and 0.06 ± 0.012 ng/ml for 24 h. Production of TNF-α (ng/ml) SEQ ID 1 (μ/ml) 6 hours 24 hours LPS alone 1.1 1.7  1 0.02 0.048  10 0.036 0.08 100 0.033 0.044 No LPS control 0.038 0.06

TABLE 9 Inhibition of E. coli LPS-induced TNF-α production by delayed addition of SEQ ID 1 to A549 cells. Peptide (20 μg/ml) was added at increasing time points to wells already containing A549 human epithelial cells and 100 ng/ml E. coli 0111:B4 LPS. The supernatant was collected after 6 hours and tested for levels of TNF-α by ELISA. The data is presented as the mean of three experiments + standard error. Time of addition of SEQ ID 1 Inhibition of after LPS (min) TNF-α (%) 0 98.3 + 0.3 15 89.3 + 3.8 30   83 + 4.6 60  68 + 8  90  53 + 8 

TABLE 10 Protection against lethal endotoxaemia in galactosamine- sensitized CD-1 mice by SEQ ID 1. CD-1 mice (9 weeks-old) were sensitized to endotoxin by three intraperitoneal injections of galactosamine (20 mg in 0.1 ml sterile PBS). Then endotoxic shock was induced by intraperitoneal injection of E. coli 0111:B4 LPS (3 μg in 0.1 ml PBS). Peptide, SEQ ID 1, (200 μg/mouse = 8 mg/kg) was injected at a separate intraperitoneal site 15 min after injection of LPS. The mice were monitored for 48 hours and the results were recorded. D-Galactosamine E. coli Peptide or Total Survival post treatment 0111:B4 LPS buffer mice endotoxin shock  0 3 μg PBS 5 5 (100%) 20 mg 3 μg PBS 12 0 (0%) 20 mg 3 μg SEQ ID 1 12 6 (50%)

TABLE 11 Protection against lethal endotoxaemia in galactosamine- sensitized CD-1 mice by Cationic Peptides. CD-1 mice (9 weeks-old) were sensitized to endotoxin by intraperitoneal injection of galactosamine (20 mg in 0.1 ml sterile PBS). Then endotoxic shock was induced by intraperitoneal injection of E. coli 0111:B4 LPS (2 μg in 0.1 ml PBS). Peptide (200 μg/mouse = 8 mg/kg) was injected at a separate intraperitoneal site 15 min after injection of LPS. The mice were monitored for 48 hours and the results were recorded. Peptide E. coli 0111:B4 Number Survival Treatment LPS added of Mice (%) Control (no peptide) 2 μg 5 0 SEQ ID 6 2 μg 5 40 SEQ ID 13 2 μg 5 20 SEQ ID 17 2 μg 5 40 SEQ ID 24 2 μg 5 0 SEQ ID 27 2 μg 5 20

TABLE 12 Protection against lethal endotoxaemia in galactosamine-sensitized BALB/c mice by Cationic Peptides. BALB/c mice (8 weeks-old) were sensitized to endotoxin by intraperitoneal injection of galactosamine (20 mg in 0.1 ml sterile PBS). Then endotoxic shock was induced by intraperitoneal injection of E. coli 0111:B4 LPS (2 μg in 0.1 ml PBS). Peptide (200 μg/mouse = 8 mg/kg) was injected at a separate intraperitoneal site 15 min after injection of LPS. The mice were monitored for 48 hours and the results were recorded. Peptide E. coli Number Survival Treatment 0111:B4 LPS added of Mice (%) No peptide 2 μg 10 10 SEQ ID 1 2 μg 6 17 SEQ ID 3 2 μg 6 0 SEQ ID 5 2 μg 6 17 SEQ ID 6 2 μg 6 17 SEQ ID 12 2 μg 6 17 SEQ ID 13 2 μg 6 33 SEQ ID 15 2 μg 6 0 SEQ ID 16 2 μg 6 0 SEQ ID 17 2 μg 6 17 SEQ ID 23 2 μg 6 0 SEQ ID 24 2 μg 6 17 SEQ ID 26 2 μg 6 0 SEQ ID 27 2 μg 6 50 SEQ ID 29 2 μg 6 0 SEQ ID 37 2 μg 6 0 SEQ ID 38 2 μg 6 0 SEQ ID 41 2 μg 6 0 SEQ ID 44 2 μg 6 0 SEQ ID 45 2 μg 6 0

TABLE 13 Protection against lethal endotoxaemia in BALB/c mice by SEQ ID 1. BALB/c mice were injected intraperitoneal with 400 μg E. coli 0111:B4 LPS. Peptide (200 μg/mouse = 8 mg/kg) was injected at a separate intraperitoneal site and the mice were monitored for 48 hours and the results were recorded. Peptide E. coli Number Survival Treatment 0111:B4 LPS of Mice (%) No peptide 400 μg 5 0 SEQ ID 1 400 μg 5 100

TABLE 14 Peptide inhibition of TNF-α production induced by S. aureus LTA. RAW 264.7 mouse macrophage cells were stimulated with 1 μg/ml S. aureus LTA in the absence and presence of increasing concentrations of peptide. The supernatant was collected and tested for levels of TNF-α by ELISA. Background levels of TNF-α production by the RAW 264.7 cells cultured with no stimuli for 6 hours resulted in TNF-α levels ranging from 0.037-0.192 ng/ml. The data is presented as the mean of three or more experiments + standard error. SEQ ID 1 added (μg/ml) Inhibition of TNF-α (%) 0.1  44.5 ± 12.5 1 76.7 ± 6.4 5 91 ± 1 10 94.5 ± 1.5 20 96 ± 1

TABLE 15 Peptide inhibition of TNF-α production induced by Mycobacterium non-capped lipoarabinomannan. RAW 264.7 mouse macrophage cells were stimulated with 1 μg/ml AraLAM in the absence and presence of 20 μg/ml peptide or Polymyxin B. The supernatant was collected and tested for levels of TNF-α by ELISA. Background levels of TNF-α production by the RAW 264.7 cells cultured with no stimuli for 6 hours resulted in TNF-α levels ranging from 0.037-0.192 ng/ml. The data is presented as the mean inhibition of three or more experiments + standard error. Peptide (20 μg/ml) Inhibition of TNF-α (%) No peptide 0 SEQ ID 1  64 ± 5.9 Polymyxin B 15 ± 2 

EXAMPLE 3 Assessment of Toxicity of the Cationic Peptides

The potential toxicity of the peptides was measured in two ways. First, the Cytotoxicity Detection Kit (Roche) (Lactate dehydrogenase-LDH) Assay was used. It is a colorimetric assay for the quantification of cell death and cell lysis, based on the measurement of LDH activity released from the cytosol of damaged cells into the supernatant. LDH is a stable cytoplasmic enzyme present in all cells and it is released into the cell culture supernatant upon damage of the plasma membrane. An increase in the amount of dead or plasma membrane-damaged cells results in an increase of the LDH enzyme activity in the culture supernatant as measured with an ELISA plate reader, OD₄₉₀ nm (the amount of color formed in the assay is proportional to the number of lysed cells). In this assay, human bronchial epithelial cells (16HBEo14, HBE) cells were incubated with 100 μg of peptide for 24 hours, the supernatant removed and tested for LDH. The other assay used to measure toxicity of the cationic peptides was the WST-1 assay (Roche). This assay is a colorimetric assay for the quantification of cell proliferation and cell viability, based on the cleavage of the tetrazolium salt WST-1 by mitochondrial dehydrogenases in viable cells (a non-radioactive alternative to the [³H]-thymidine incorporation assay). In this assay, HBE cells were incubated with 100 μg of peptide for 24 hours, and then 10 μl/well Cell Proliferation Reagent WST-1 was added. The cells are incubated with the reagent and the plate is then measured with an ELISA plate reader, OD₄₉₀ nm.

The results shown below in Tables 16 and 17 demonstrate that most of the peptides are not toxic to the cells tested. However, four of the peptides from Formula F (SEQ ID NOS: 40, 41, 42 and 43) did induce membrane damage as measured by both assays.

TABLE 16 Toxicity of the Cationic Peptides as Measured by the LDH Release Assay. Human HBE bronchial epithelial cells were incubated with 100 μg/ml peptide or Polymyxin B for 24 hours. LDH activity was assayed in the supernatant of the cell cultures. As a control for 100% LDH release, Triton X-100 was added. The data is presented as the mean ± standard deviation. Only peptides SEQ ID 40, 41, 42 and 43 showed any significant toxicity. Treatment LDH Release (OD₄₉₀ nm) No cells Control 0.6 ± 0.1 Triton X-100 Control 4.6 ± 0.1 No peptide control  1.0 ± 0.05 SEQ ID 1 1.18 ± 0.05 SEQ ID 3 1.05 ± 0.04 SEQ ID 6 0.97 ± 0.02 SEQ ID 7 1.01 ± 0.04 SEQ ID 9  1.6 ± 0.03 SEQ ID 10 1.04 ± 0.04 SEQ ID 13 0.93 ± 0.06 SEQ ID 14 0.99 ± 0.05 SEQ ID 16 0.91 ± 0.04 SEQ ID 17 0.94 ± 0.04 SEQ ID 19 1.08 ± 0.02 SEQ ID 20 1.05 ± 0.03 SEQ ID 21 1.06 ± 0.04 SEQ ID 22 1.29 ± 0.12 SEQ ID 23 1.26 ± 0.46 SEQ ID 24 1.05 ± 0.01 SEQ ID 26 0.93 ± 0.04 SEQ ID 27 0.91 ± 0.04 SEQ ID 28 0.96 ± 0.06 SEQ ID 29 0.99 ± 0.02 SEQ ID 31 0.98 ± 0.03 SEQ ID 33 1.03 ± 0.05 SEQ ID 34 1.02 ± 0.03 SEQ ID 35 0.88 ± 0.03 SEQ ID 36 0.85 ± 0.04 SEQ ID 37 0.96 ± 0.04 SEQ ID 38 0.95 ± 0.02 SEQ ID 40 2.8 ± 0.5 SEQ ID 41 3.3 ± 0.2 SEQ ID 42 3.4 ± 0.2 SEQ ID 43 4.3 ± 0.2 SEQ ID 44 0.97 ± 0.03 SEQ ID 45 0.98 ± 0.04 SEQ ID 47 1.05 ± 0.05 SEQ ID 48 0.95 ± 0.05 SEQ ID 53 1.03 ± 0.06 Polymyxin B 1.21 ± 0.03

TABLE 17 Toxicity of the Cationic Peptides as Measured by the WST-1 Assay. HBE cells were incubated with 100 μg/ml peptide or Polymyxin B for 24 hours and cell viability was tested. The data is presented as the mean ± standard deviation. As a control for 100% LDH release, Triton X-100 was added. Only peptides SEQ ID 40, 41, 42 and 43 showed any significant toxicity. Treatment OD₄₉₀ nm No cells Control 0.24 ± 0.01 Triton X-100 Control 0.26 ± 0.01 No peptide control 1.63 ± 0.16 SEQ ID 1 1.62 ± 0.34 SEQ ID 3 1.35 ± 0.12 SEQ ID 10 1.22 ± 0.05 SEQ ID 6 1.81 ± 0.05 SEQ ID 7 1.78 ± 0.10 SEQ ID 9 1.69 ± 0.29 SEQ ID 13 1.23 ± 0.11 SEQ ID 14 1.25 ± 0.02 SEQ ID 16 1.39 ± 0.26 SEQ ID 17 1.60 ± 0.46 SEQ ID 19 1.42 ± 0.15 SEQ ID 20 1.61 ± 0.21 SEQ ID 21 1.28 ± 0.07 SEQ ID 22 1.33 ± 0.07 SEQ ID 23 1.14 ± 0.24 SEQ ID 24 1.27 ± 0.16 SEQ ID 26 1.42 ± 0.11 SEQ ID 27 1.63 ± 0.03 SEQ ID 28 1.69 ± 0.03 SEQ ID 29 1.75 ± 0.09 SEQ ID 31 1.84 ± 0.06 SEQ ID 33 1.75 ± 0.21 SEQ ID 34 0.96 ± 0.05 SEQ ID 35 1.00 ± 0.08 SEQ ID 36 1.58 ± 0.05 SEQ ID 37 1.67 ± 0.02 SEQ ID 38 1.83 ± 0.03 SEQ ID 40 0.46 ± 0.06 SEQ ID 41 0.40 ± 0.01 SEQ ID 42 0.39 ± 0.08 SEQ ID 43 0.46 ± 0.10 SEQ ID 44 1.49 ± 0.39 SEQ ID 45 1.54 ± 0.35 SEQ ID 47 1.14 ± 0.23 SEQ ID 48 0.93 ± 0.08 SEQ ID 53 1.51 ± 0.37 Polymyxin B 1.30 ± 0.13

EXAMPLE 4 Polynucleotide Regulation by Cationic Peptides

Polynucleotide arrays were utilized to determine the effect of cationic peptides by themselves on the transcriptional response of macrophages and epithelial cells. Mouse macrophage RAW 264.7, Human Bronchial cells (HBE), or A549 human epithelial cells were plated in 150 mm tissue culture dishes at 5.6×10⁶ cells/dish, cultured overnight and then incubated with 50 μg/ml peptide or medium alone for 4 h. After stimulation, the cells were washed once with diethyl pyrocarbonate-treated PBS, and detached from the dish using a cell scraper. Total RNA was isolated using Trizol (Gibco Life Technologies). The RNA pellet was resuspended in RNase-free water containing RNase inhibitor (Ambion, Austin, Tex.). The RNA was treated with DNaseI (Clontech, Palo Alto, Calif.) for 1 h at 37° C. After adding termination mix (0.1 M EDTA [pH 8.0], 1 mg/ml glycogen), the samples were extracted once with phenol: chloroform: isoamyl alcohol (25:24:1), and once with chloroform. The RNA was then precipitated by adding 2.5 volumes of 100% ethanol and 1/10^(th) volume sodium acetate, pH 5.2. The RNA was resuspended in RNase-free water with RNase inhibitor (Ambion) and stored at −70° C. The quality of the RNA was assessed by gel electrophoresis on a 1% agarose gel. Lack of genomic DNA contamination was assessed by using the isolated RNA as a template for PCR amplification with β-actin-specific primers (5′-GTCCCTGTATGCCTCTGGTC-3′ (SEQ ID NO: 55) and 5′-GATGTCACGCACGATTTCC-3′ (SEQ ID NO: 56)). Agarose gel electrophoresis and ethidium bromide staining confirmed the absence of an amplicon after 35 cycles.

Atlas cDNA Expression Arrays (Clontech, Palo Alto, Calif.), which consist of 588 selected mouse cDNAs spotted in duplicate on positively charged membranes were used for early polynucleotide array studies (Tables 18, 19). ³²P-radiolabeled cDNA probes prepared from 5 μg total RNA were incubated with the arrays overnight at 71° C. The filters were washed extensively and then exposed to a phosphoimager screen (Molecular Dynamics, Sunnyvale, Calif.) for 3 days at 4° C. The image was captured using a Molecular Dynamics PSI phosphoimager. The hybridization signals were analyzed using AtlasImage 1.0 Image Analysis software (Clontech) and Excel (Microsoft, Redmond, Wash.). The intensities for each spot were corrected for background levels and normalized for differences in probe labeling using the average values for 5 polynucleotides observed to vary little between the stimulation conditions: β-actin, ubiquitin, ribosomal protein S29, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and Ca²⁺ binding protein. When the normalized hybridization intensity for a given cDNA was less than 20, it was assigned a value of 20 to calculate the ratios and relative expression.

The next polynucleotide arrays used (Tables 21-26) were the Resgen Human cDNA arrays (identification number for the genome is PRHU03-S3), which consist of 7,458 human cDNAs spotted in duplicate. Probes were prepared from 15-20 μg of total RNA and labeled with Cy3 labeled dUTP. The probes were purified and hybridized to printed glass slides overnight at 42° C. and washed. After washing, the image was captured using a Virtek slide reader. The image processing software (Imagene 4.1, Marina Del Rey, Calif.) determines the spot mean intensity, median intensities, and background intensities. Normalization and analysis was performed with Genespring software (Redwood City, Calif.). Intensity values were calculated by subtracting the mean background intensity from the mean intensity value determined by Imagene. The intensities for each spot were normalized by taking the median spot intensity value from the population of spot values within a slide and comparing this value to the values of all slides in the experiment. The relative changes seen with cells treated with peptide compared to control cells can be found in the Tables below.

The other polynucleotide arrays used (Tables 27-35) were the Human Operon arrays (identification number for the genome is PRHU04-S1), which consist of about 14,000 human oligos spotted in duplicate. Probes were prepared from 10 μg of total RNA and labeled with Cy3 or Cy5 labeled dUTP. In these experiments, A549 epithelial cells were plated in 100 mm tissue culture dishes at 2.5×10⁶ cells/dish. Total RNA was isolated using RNAqueous (Ambion). DNA contamination was removed with DNA-free kit (Ambion). The probes prepared from total RNA were purified and hybridized to printed glass slides overnight at 42° C. and washed. After washing, the image was captured using a Perkin Elmer array scanner. The image processing software (Imagene 5.0, Marina Del Rey, Calif.) determines the spot mean intensity, median intensities, and background intensities. An “in house” program was used to remove background. The program calculates the bottom 10% intensity for each subgrid and subtracts this for each grid. Analysis was performed with Genespring software (Redwood City, Calif.). The intensities for each spot were normalized by taking the median spot intensity value from the population of spot values within a slide and comparing this value to the values of all slides in the experiment. The relative changes seen with cells treated with peptide compared to control cells can be found in the Tables below.

Semi-quantitative RT-PCR was performed to confirm polynucleotide array results. 1 μg RNA samples were incubated with 1 μl oligodT (500 μg/ml) and 1 μl mixed dNTP stock at 1 mM, in a 12 μl volume with DEPC treated water at 65° C. for 5 min in a thermocycler. 4 μl 5× First Strand buffer, 2 μl 0.1M DTT, and 1 μl RNaseOUT recombinant ribonuclease inhibitor (40 units/μl) were added and incubated at 42° C. for 2 min, followed by the addition of 1 μl (200 units) of Superscript II (Invitrogen, Burlington, ON). Negative controls for each RNA source were generated using parallel reactions in the absence of Superscript II. cDNAs were amplified in the presence of 5′ and 3′ primers (1.0 μM), 0.2 mM dNTP mixture, 1.5 mM MgCl, 1 U of Taq DNA polymerase (New England Biolabs, Missisauga, ON), and 1×PCR buffer. Each PCR was performed with a thermal cycler by using 30-40 cycles consisting of 30 s of denaturation at 94° C., 30 s of annealing at either 52° C. or 55° C. and 40 s of extension at 72° C. The number of cycles of PCR was optimized to lie in the linear phase of the reaction for each primer and set of RNA samples. A housekeeping polynucleotide β-actin was amplified in each experiment to evaluate extraction procedure and to estimate the amount of RNA. The reaction product was visualized by electrophoresis and analyzed by densitometry, with relative starting RNA concentrations calculated with reference to β-actin amplification.

Table 18 demonstrates that SEQ ID NO: 1 treatment of RAW 264.7 cells up-regulated the expression of more than 30 different polynucleotides on small Atlas microarrays with selected known polynucleotides. The polynucleotides up-regulated by peptide, SEQ ID NO: 1, were mainly from two categories: one that includes receptors (growth, chemokine, interleukin, interferon, hormone, neurotransmitter), cell surface antigens and cell adhesion and another one that includes cell-cell communication (growth factors, cytokines, chemokines, interleukin, interferons, hormones), cytoskeleton, motility, and protein turnover. The specific polynucleotides up-regulated included those encoding chemokine MCP-3, the anti-inflammatory cytokine IL-10, macrophage colony stimulating factor, and receptors such as IL-1R-2 (a putative antagonist of productive IL-1 binding to IL-1R1), PDGF receptor B, NOTCH4, LIF receptor, LFA-1, TGFβ receptor 1, G-CSF receptor, and IFNγ receptor. The peptide also up-regulated polynucleotides encoding several metalloproteinases, and inhibitors thereof, including the bone morphogenetic proteins BMP-1, BMP-2, BMP-8a, TIMP2 and TIMP3. As well, the peptide up-regulated specific transcription factors, including JunD, and the YY and LIM-1 transcription factors, and kinases such as Etk1 and Csk demonstrating its widespread effects. It was also discovered from the polynucleotide array studies that SEQ ID NO: 1 down-regulated at least 20 polynucleotides in RAW 264.7 macrophage cells (Table 19). The polynucleotides down-regulated by peptide included DNA repair proteins and several inflammatory mediators such as MIP-1α, oncostatin M and IL-12. A number of the effects of peptide on polynucleotide expression were confirmed by RT-PCR (Table 20). The peptides, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 19, and SEQ ID NO: 1, and representative peptides from each of the formulas also altered the transcriptional responses in a human epithelial cell line using mid-sized microarrays (7835 polynucleotides). The effect of SEQ ID NO: 1 on polynucleotide expression was compared in 2 human epithelial cell lines, A549 and HBE. Polynucleotides related to the host immune response that were up-regulated by 2 peptides or more by a ratio of 2-fold more than unstimulated cells are described in Table 21. Polynucleotides that were down-regulated by 2 peptides or more by a ratio of 2-fold more than unstimulated cells are described in Table 22. In Table 23 and Table 24, the human epithelial pro-inflammatory polynucleotides that are up- and down-regulated respectively are shown. In Table 25 and Table 26 the anti-inflammatory polynucleotides affected by cationic peptides are shown. The trend becomes clear that the cationic peptides up-regulate the anti-inflammatory response and down-regulate the pro-inflammatory response. It was very difficult to find a polynucleotide related to the anti-inflammatory response that was down-regulated (Table 26). The pro-inflammatory polynucleotides upregulated by cationic peptides were mainly polynucleotides related to migration and adhesion. Of the down-regulated pro-inflammatory polynucleotides, it should be noted that all the cationic peptides affected several toll-like receptor (TLR) polynucleotides, which are very important in signaling the host response to infectious agents. An important anti-inflammatory polynucleotide that was up-regulated by all the peptides is the IL-10 receptor. IL-10 is an important cytokine involved in regulating the pro-inflammatory cytokines. These polynucleotide expression effects were also observed using primary human macrophages as observed for peptide SEQ ID NO: 6 in Tables 27 and 28. The effect of representative peptides from each of the formulas on human epithelial cell expression of selected polynucleotides (out of 14,000 examined) is shown in Tables 31-37 below. At least 6 peptides from each formula were tested for their ability to alter human epithelial polynucleotide expression and indeed they had a wide range of stimulatory effects. In each of the formulas there were at least 50 polynucleotides commonly up-regulated by each of the peptides in the group.

TABLE 18 Polynucleotides up-regulated by peptide, SEQ ID NO: 1, treatment of RAW macrophage cells^(a). The cationic peptides at a concentration of 50 μg/ml were shown to potently induce the expression of several polynucleotides. Peptide was incubated with the RAW cells for 4 h and the RNA was isolated, converted into labeled cDNA probes and hybridized to Atlas arrays. The intensity of unstimulated cells is shown in the third column. The “Ratio Peptide: Unstimulated” column refers to the intensity of polynucleotide expression in peptide-simulated cells divided by the intensity of unstimulated cells. The changes in the normalized intensities of the housekeeping polynucleotides ranged from 0.8-1.2 fold, validating the use of these polynucleotides for normalization. When the normalized hybridization intensity for a given cDNA was less than 20, it was assigned a value of 20 to calculate the ratios and relative expression. The array experiments were repeated 3 times with different RNA preparations and the average fold change is shown above. Polynucleotides with a two fold or greater change in relative expression levels are presented. Polynucleo- Polynucleo- Ratio tide/ tide Unstimulated peptide: Accession Protein Function Intensity Unstimulated^(b) Number Etk1 Tyrosine-protein kinase 20 43 M68513 receptor PDGFRB Growth factor receptor 24 25 X04367 Corticotropin releasing 20 23 X72305 factor receptor NOTCH4 proto-oncopolynucleotide 48 18 M80456 IL-1R2 Interleukin receptor 20 16 X59769 MCP-3 Chemokine 56 14 S71251 BMP-1 Bone 20 14 L24755 morphopolynucleotidetic protein Endothelin Receptor 20 14 U32329 b receptor c-ret Oncopolynucleotide 20 13 X67812 precursor LIFR Cytokine receptor 20 12 D26177 BMP-8a Bone 20 12 M97017 morphopolynucleotidetic protein Zfp92 Zinc finger protein 92 87 11 U47104 MCSF Macrophage colony 85 11 X05010 stimulating factor 1 GCSFR Granulocyte colony- 20 11 M58288 stimulating factor receptor IL-8RB Chemokine receptor 112 10 D17630 IL-9R Interleukin receptor 112 6 M84746 Cas Crk-associated substrate 31 6 U48853 p58/GTA Kinase 254 5 M58633 CASP2 Caspase precursor 129 5 D28492 IL-1β Interleukin precursor 91 5 M15131 precursor SPI2-2 Serine protease inhibitor 62 5 M64086 C5AR Chemokine receptor 300 4 S46665 L-myc Oncopolynucleotide 208 4 X13945 IL-10 Interleukin 168 4 M37897 p19ink4 cdk4 and cdk6 inhibitor 147 4 U19597 ATOH2 Atonal homolog 2 113 4 U29086 DNAse1 DNase 87 4 U00478 CXCR-4 Chemokine receptor 36 4 D87747 Cyclin D3 Cyclin 327 3 U43844 IL-7Rα Interleukin receptor 317 3 M29697 POLA DNA polymerase _(α) 241 3 D17384 Tie-2 Oncopolynucleotide 193 3 S67051 DNL1 DNA ligase I 140 3 U04674 BAD Apoptosis protein 122 3 L37296 GADD45 DNA-damage-inducible 88 3 L28177 protein Sik Src-related kinase 82 3 U16805 integrin_(α)4 Integrin 2324 2 X53176 TGFβR1 Growth factor receptor 1038 2 D25540 LAMR1 Receptor 1001 2 J02870 Crk Crk adaptor protein 853 2 S72408 ZFX Chromosomal protein 679 2 M32309 Cyclin E1 Cylcin 671 2 X75888 POLD1 DNA polymerase subunit 649 2 Z21848 Vav proto-oncopolynucleotide 613 2 X64361 YY(NF-E1) Transcription factor 593 2 L13968 JunD Transcription factor 534 2 J050205 Csk c-src kinase 489 2 U05247 Cdk7 Cyclin-dependent kinase 475 2 U11822 MLC1A Myosin light subunit 453 2 M19436 isoform ERBB-3 Receptor 435 2 L47240 UBF Transcription factor 405 2 X60831 TRAIL Apoptosis ligand 364 2 U37522 LFA-1 Cell adhesion receptor 340 2 X14951 SLAP Src-like adaptor protein 315 2 U29056 IFNGR Interferon gamma receptor 308 2 M28233 LIM-1 Transcription factor 295 2 Z27410 ATF2 Transcription factor 287 2 S76657 FST Follistatin precursor 275 2 Z29532 TIMP3 Protease inhibitor 259 2 L19622 RU49 Transcription factor 253 2 U41671 IGF-1Rα Insulin-like growth 218 2 U00182 factor receptor Cyclin G2 Cyclin 214 2 U95826 fyn Tyrosine-protein kinase 191 2 U70324 BMP-2 Bone 186 2 L25602 morphopolynucleotidetic protein Brn-3.2 Transcription factor 174 2 S68377 POU KIF1A Kinesin family protein 169 2 D29951 MRC1 Mannose receptor 167 2 Z11974 PAI2 Protease inhibitor 154 2 X19622 BKLF CACCC Box-binding protein 138 2 U36340 TIMP2 Protease inhibitor 136 2 X62622 Mas Proto-oncopolynucleotide 131 2 X67735 NURR-1 Transcription factor 129 2 S53744

TABLE 19 Polynucleotides down-regulated by SEQ ID NO: 1 treatment of RAW macrophage cells^(a). The cationic peptides at a concentration of 50 μg/ml were shown to reduce the expression of several polynucleotides. Peptide was incubated with the RAW cells for 4 h and the RNA was isolated, converted into labeled cDNA probes and hybridized to Atlas arrays. The intensity of unstimulated cells is shown in the third column. The “Ratio Peptide: Unstimulated” column refers to the intensity of polynucleotide expression in peptide-simulated cells divided by the intensity of unstimulated cells. The array experiments were repeated 3 times with different cells and the average fold change is shown below. Polynucleotides with an approximately two fold or greater change in relative expression levels are presented. Ratio Polynucleotide/ Polynucleotide Unstimulated peptide: Accession Protein Function Intensity Unstimulated Number sodium channel Voltage-gated ion channel 257 0.08 L36179 XRCC1 DNA repair protein 227 0.09 U02887 ets-2 Oncopolynucleotide 189 0.11 J04103 XPAC DNA repair protein 485 0.12 X74351 EPOR Receptor precursor 160 0.13 J04843 PEA 3 Ets-related protein 158 0.13 X63190 orphan receptor Nuclear receptor 224 0.2 U11688 N-cadherin Cell adhesion receptor 238 0.23 M31131 OCT3 Transcription factor 583 0.24 M34381 PLCβ phospholipase 194 0.26 U43144 KRT18 Intermediate filament 318 0.28 M11686 proteins THAM Enzyme 342 0.32 X58384 CD40L CD40 ligand 66 0.32 X65453 CD86 T-lymphocyte antigen 195 0.36 L25606 oncostatin M Cytokine 1127 0.39 D31942 PMS2 DNA DNA repair protein 200 0.4 U28724 IGFBP6 Growth factor 1291 0.41 X81584 MIP-1β Cytokine 327 0.42 M23503 ATBF1 AT motif-binding factor 83 0.43 D26046 nucleobindin Golgi resident protein 367 0.43 M96823 bcl-x Apoptosis protein 142 0.43 L35049 uromodulin glycoprotein 363 0.47 L33406 IL-12 p40 Interleukin 601 0.48 M86671 MmRad52 DNA repair protein 371 0.54 Z32767 Tob1 Antiproliferative factor 956 0.5 D78382 Ung1 DNA repair protein 535 0.51 X99018 KRT19 Intermediate filament 622 0.52 M28698 proteins PLCγ phospholipase 251 0.52 X95346 Integrin α₆ Cell adhesion receptor 287 0.54 X69902 GLUT1 Glucose transporter 524 0.56 M23384 CTLA4 immunoglobin 468 0.57 X05719 superfamily FRA2 Fos-related antigen 446 0.57 X83971 MTRP Lysosome-associated 498 0.58 U34259 protein

TABLE 20 Polynucleotide Expression changes in response to peptide, SEQ ID NO: 1, could be confirmed by RT-PCR. RAW 264.7 macrophage cells were incubated with 50 μg/ml of peptide or media only for 4 hours and total RNA isolated and subjected to semi-quantitative RT-PCR. Specific primer pairs for each polynucleotide were used for amplification of RNA. Amplification of β-actin was used as a positive control and for standardization. Densitometric analysis of RT-PCR products was used. The results refer to the relative fold change in polynucleotide expression of peptide treated cells compared to cells incubated with media alone. The data is presented as the mean ± standard error of three experiments. Polynucleotide Array Ratio-* RT-PCR Ratio -* CXCR-4 4.0 ± 1.7 4.1 ± 0.9 IL-8RB 9.5 ± 7.6 7.1 ± 1.4 MCP-3 13.5 ± 4.4   4.8 ± 0.88 IL-10 4.2 ± 2.1 16.6 ± 6.1  CD14 0.9 ± 0.1 0.8 ± 0.3 MIP-1B 0.42 ± 0.09 0.11 ± 0.04 XRCC1 0.12 ± 0.01  0.25 ± 0.093 MCP-1 Not on array 3.5 ± 1.4

TABLE 21 Polynucleotides up-regulated by peptide treatment of A549 epithelial cells^(a). The cationic peptides at concentrations of 50 μg/ml were shown to increase the expression of several polynucleotides. Peptide was incubated with the human A549 epithelial cells for 4 h and the RNA was isolated, converted into labeled cDNA probes and hybridized to Human cDNA arrays ID#PRHU03-S3. The intensity of polynucleotides in unstimulated cells is shown in the second column. The “Ratio Peptide: Unstimulated” columns refers to the intensity of polynucleotide expression in peptide- simulated cells divided by the intensity of unstimulated cells. Unstimulated Ratio Peptide: Unstimulated Accession Polynucleotide/Protein Intensity ID 2 ID 3 ID 19 ID 1 Number IL-1 R antagonist homolog 1 0.00 3086 1856 870 AI167887 IL-10 R beta 0.53 2.5 1.6 1.9 3.1 AA486393 IL-11 R alpha 0.55 2.4 1.0 4.9 1.8 AA454657 IL-17 R 0.54 2.1 2.0 1.5 1.9 AW029299 TNF R superfamily, member 1B 0.28 18 3.0 15 3.6 AA150416 TNF R superfamily, member 5 33.71 3.0 0.02 H98636 (CD40LR) TNF R superfamily, member 11b 1.00 5.3 4.50 0.8 AA194983 IL-8 0.55 3.6 17 1.8 1.1 AA102526 interleukin enhancer binding factor 2 0.75 1.3 2.3 0.8 4.6 AA894687 interleukin enhancer binding factor 1 0.41 2.7 5.3 2.5 R56553 cytokine inducible SH2-containing 0.03 33 44 39 46 AA427521 protein IK cytokine, down-regulator of 0.50 3.1 2.0 1.7 3.3 R39227 HLA II cytokine inducible SH2-containing 0.03 33 44 39 46 AA427521 protein IK cytokine, down-regulator of 0.50 3.1 2.0 1.7 3.3 R39227 HLA II small inducible cytokine subfamily 1.00 3.9 2.4 AI922341 A (Cys-Cys), member 21 TGFB inducible early growth 0.90 2.4 2.1 0.9 1.1 AI473938 response 2 NK cell R 1.02 2.5 0.7 0.3 1.0 AA463248 CCR6 0.14 4.5 7.8 6.9 7.8 N57964 cell adhesion molecule 0.25 4.0 3.9 3.9 5.1 R40400 melanoma adhesion molecule 0.05 7.9 20 43 29.1 AA497002 CD31 0.59 2.7 3.1 1.0 1.7 R22412 integrin, alpha 2 (CD49B, alpha 2 1.00 0.9 2.4 3.6 0.9 AA463257 subunit of VLA-2 receptor integrin, alpha 3 (antigen CD49C, 0.94 0.8 2.5 1.9 1.1 AA424695 alpha 3 subunit of VLA-3 receptor) integrin, alpha E 0.01 180 120 28 81 AA425451 integrin, beta 1 0.47 2.1 2.1 7.0 2.6 W67174 integrin, beta 3 0.55 2.7 2.8 1.8 1.0 AA037229 integrin, beta 3 0.57 2.6 1.4 1.8 2.0 AA666269 integrin, beta 4 0.65 0.8 2.2 4.9 1.5 AA485668 integrin beta 4 binding protein 0.20 1.7 5.0 6.6 5.3 AI017019 calcium and integrin binding protein 0.21 2.8 4.7 9.7 6.7 AA487575 disintegrin and metalloproteinase 0.46 3.1 2.2 3.8 AA279188 domain 8 disintegrin and metalloproteinase 0.94 1.1 2.3 3.6 0.5 H59231 domain 9 disintegrin and metalloproteinase 0.49 1.5 2.1 3.3 2.2 AA043347 domain 10 disintegrin and metalloproteinase 0.44 1.9 2.3 2.5 4.6 H11006 domain 23 cadherin 1, type 1, E-cadherin 0.42 8.1 2.2 2.4 7.3 H97778 (epithelial) cadherin 12, type 2 (N-cadherin 2) 0.11 13 26 9.5 AI740827 protocadherin 12 0.09 14.8 11.5 2.6 12.4 AI652584 protocadherin gamma subfamily C, 3 0.34 3.0 2.5 4.5 9.9 R89615 catenin (cadherin-associated 0.86 1.2 2.2 2.4 AA025276 protein), delta 1 laminin R 1 (67 kD, ribosomal 0.50 0.4 2.0 4.4 3.0 AA629897 protein SA) killer cell lectin-like receptor 0.11 9.7 9.0 4.1 13.4 AA190627 subfamily C, member 2 killer cell lectin-like receptor 1.00 3.2 1.0 0.9 1.3 W93370 subfamily C, member 3 killer cell lectin-like receptor 0.95 2.3 1.7 0.7 1.1 AI433079 subfamily G, member 1 C-type lectin-like receptor-2 0.45 2.1 8.0 2.2 5.3 H70491 CSF 3 R 0.40 1.9 2.5 3.5 4.0 AA458507 macrophage stimulating 1 R 1.00 1.7 2.3 0.4 0.7 AA173454 BMP R type IA 0.72 1.9 2.8 0.3 1.4 W15390 formyl peptide receptor 1 1.00 3.1 1.4 0.4 AA425767 CD2 1.00 2.6 0.9 1.2 0.9 AA927710 CD36 0.18 8.2 5.5 6.2 2.5 N39161 vitamin D R 0.78 2.5 1.3 1.1 1.4 AA485226 Human proteinase activated R-2 0.54 6.1 1.9 2.2 AA454652 prostaglandin E receptor 3 (subtype 0.25 4.1 4.9 3.8 4.9 AA406362 EP3) PDGF R beta polypeptide 1.03 2.5 1.0 0.5 0.8 R56211 VIP R 2 1.00 3.1 2.0 AI057229 growth factor receptor-bound 0.51 2.2 2.0 2.4 0.3 AA449831 protein 2 Mouse Mammary Turmor Virus 1.00 6.9 16 W93891 Receptor homolog adenosine A2a R 0.41 3.1 1.8 4.0 2.5 N57553 adenosine A3 R 0.83 2.0 2.3 1.0 1.2 AA863086 T cell R delta locus 0.77 2.7 1.3 1.8 AA670107 prostaglandin E receptor 1 (subtype 0.65 7.2 6.0 1.5 AA972293 EP1) growth factor receptor-bound 0.34 3.0 6.3 2.9 R24266 protein 14 Epstein-Barr virus induced 0.61 1.6 2.4 8.3 AA037376 polynucleotide 2 complement component receptor 2 0.22 26 4.5 2.6 18.1 AA521362 endothelin receptor type A 0.07 12 14 14 16 AA450009 v-SNARE R 0.56 11 12 1.8 AA704511 tyrosine kinase, non-receptor, 1 0.12 7.8 8.5 10 8.7 AI936324 receptor tyrosine kinase-like orphan 0.40 7.3 5.0 1.6 2.5 N94921 receptor 2 protein tyrosine phosphatase, non- 1.02 1.0 13.2 0.5 0.8 AA682684 receptor type 3 protein tyrosine phosphatase, non- 0.28 3.5 4.0 0.9 5.3 AA434420 receptor type 9 protein tyrosine phosphatase, non- 0.42 2.9 2.4 2.2 3.0 AA995560 receptor type 11 protein tyrosine phosphatase, non- 1.00 2.3 2.2 0.8 0.5 AA446259 receptor type 12 protein tyrosine phosphatase, non- 0.58 1.7 2.4 3.6 1.7 AA679180 receptor type 13 protein tyrosine phosphatase, non- 0.52 3.2 0.9 1.9 6.5 AI668897 receptor type 18 protein tyrosine phosphatase, 0.25 4.0 2.4 16.8 12.8 H82419 receptor type, A protein tyrosine phosphatase, 0.60 3.6 3.2 1.6 1.0 AA045326 receptor type, J protein tyrosine phosphatase, 0.73 1.2 2.8 3.0 1.4 R52794 receptor type, T protein tyrosine phosphatase, 0.20 6.1 1.2 5.6 5.0 AA644448 receptor type, U protein tyrosine phosphatase, 1.00 5.1 2.4 AA481547 receptor type, C-associated protein phospholipase A2 receptor 1 0.45 2.8 2.2 1.9 2.2 AA086038 MAP kinase-activated protein 0.52 2.1 2.7 1.1 1.9 W68281 kinase 3 MAP kinase kinase 6 0.10 18 9.6 32 H07920 MAP kinase kinase 5 1.00 3.0 5.2 0.8 0.2 W69649 MAP kinase 7 0.09 11.5 12 33 H39192 MAP kinase 12 0.49 2.1 1.7 2.2 2.0 AI936909 G protein-coupled receptor 4 0.40 3.7 3.0 2.4 2.5 AI719098 G protein-coupled receptor 49 0.05 19 19 27 AA460530 G protein-coupled receptor 55 0.08 19 15 12 N58443 G protein-coupled receptor 75 0.26 5.2 3.1 7.1 3.9 H84878 G protein-coupled receptor 85 0.20 6.8 5.4 4.9 5.0 N62306 regulator of G-protein signalling 20 0.02 48 137 82 AI264190 regulator of G-protein signalling 6 0.27 3.7 8.9 10.6 R39932 BCL2-interacting killer (apoptosis- 1.00 1.9 5.2 AA291323 inducing) apoptosis inhibitor 5 0.56 2.8 1.6 2.4 1.8 AI972925 caspase 6, apoptosis-related 0.79 0.7 2.6 1.3 2.8 W45688 cysteine protease apoptosis-related protein PNAS-1 0.46 2.2 1.4 2.3 2.9 AA521316 caspase 8, apoptosis-related 0.95 2.2 1.0 0.6 2.0 AA448468 cysteine protease

TABLE 22 Polynucleotides down-regulated by peptide treatment of A549 epithelial cells^(a). The cationic peptides at concentrations of 50 μg/ml were shown to decrease the expression of several polynucleotides. Peptide was incubated with the human A549 epithelial cells for 4 h and the RNA was isolated, converted into labeled cDNA probes and hybridized to Human cDNA arrays ID#PRHU03-S3. The intensity of polynucleotides in unstimulated cells is shown in the second column. The “Ratio Peptide: Unstimulated” columns refers to the intensity of polynucleotide expression in peptide- simulated cells divided by the intensity of unstimulated cells. Unstimulated Ratio Peptide: Unstimulated Accession Polynucleotide/Protein Intensity ID 2 ID 3 ID 19 ID 1 Number TLR 1 3.22 0.35 0.31 0.14 0.19 AI339155 TLR 2 2.09 0.52 0.31 0.48 0.24 T57791 TLR 5 8.01 0.12 0.39 N41021 TLR 7 5.03 0.13 0.11 0.20 0.40 N30597 TNF receptor-associated factor 2 0.82 1.22 0.45 2.50 2.64 T55353 TNF receptor-associated factor 3 3.15 0.15 0.72 0.32 AA504259 TNF receptor superfamily, member 12 4.17 0.59 0.24 0.02 W71984 TNF R superfamily, member 17 2.62 0.38 0.55 0.34 AA987627 TRAF and TNF receptor-associated 1.33 0.75 0.22 0.67 0.80 AA488650 protein IL-1 receptor, type I 1.39 0.34 0.72 1.19 0.34 AA464526 IL-2 receptor, alpha 2.46 0.41 0.33 0.58 AA903183 IL-2 receptor, gamma (severe combined 3.34 0.30 0.24 0.48 N54821 immunodeficiency) IL-12 receptor, beta 2 4.58 0.67 0.22 AA977194 IL-18 receptor 1 1.78 0.50 0.42 0.92 0.56 AA482489 TGF beta receptor III 2.42 0.91 0.24 0.41 0.41 H62473 leukotriene b4 receptor (chemokine 1.00 1.38 4.13 0.88 AI982606 receptor-like 1) small inducible cytokine subfamily A 2.26 0.32 0.44 1.26 AA495985 (Cys-Cys), member 18 small inducible cytokine subfamily A 2.22 0.19 0.38 0.45 0.90 AI285199 (Cys-Cys), member 20 small inducible cytokine subfamily A 2.64 0.38 0.31 1.53 AA916836 (Cys-Cys), member 23 small inducible cytokine subfamily B 3.57 0.11 0.06 0.28 0.38 AI889554 (Cys-X-Cys), member 6 (granulocyte chemotactic protein 2) small inducible cytokine subfamily B 2.02 0.50 1.07 0.29 0.40 AA878880 (Cys-X-Cys), member 10 small inducible cytokine A3 2.84 1.79 0.32 0.35 AA677522 (homologous to mouse Mip-1a) cytokine-inducible kinase 2.70 0.41 0.37 0.37 0.34 AA489234 complement component C1q receptor 1.94 0.46 0.58 0.51 0.13 AI761788 cadherin 11, type 2, OB-cadherin 2.00 0.23 0.57 0.30 0.50 AA136983 (osteoblast) cadherin 3, type 1, P-cadherin 2.11 0.43 0.53 0.10 0.47 AA425217 (placental) cadherin, EGF LAG seven-pass G-type 1.67 0.42 0.41 1.21 0.60 H39187 receptor 2, flamingo (Drosophila) homolog cadherin 13, H-cadherin (heart) 1.78 0.37 0.40 0.56 0.68 R41787 selectin L (lymphocyte adhesion 4.43 0.03 0.23 0.61 H00662 molecule 1) vascular cell adhesion molecule 1 1.40 0.20 0.72 0.77 0.40 H16591 intercellular adhesion molecule 3 1.00 0.12 0.31 2.04 1.57 AA479188 integrin, alpha 1 2.42 0.41 0.26 0.56 AA450324 integrin, alpha 7 2.53 0.57 0.39 0.22 0.31 AA055979 integrin, alpha 9 1.16 0.86 0.05 0.01 2.55 AA865557 integrin, alpha 10 1.00 0.33 0.18 1.33 2.25 AA460959 integrin, beta 5 1.00 0.32 1.52 1.90 0.06 AA434397 integrin, beta 8 3.27 0.10 1.14 0.31 0.24 W56754 disintegrin and metalloproteinase 2.50 0.40 0.29 0.57 0.17 AI205675 domain 18 disintegrin-like and metalloprotease 2.11 0.32 0.63 0.47 0.35 AA398492 with thrombospondin type 1 motif, 3 disintegrin-like and metalloprotease 1.62 0.39 0.42 1.02 0.62 AI375048 with thrombospondin type 1 motif, 5 T-cell receptor interacting molecule 1.00 0.41 1.24 1.41 0.45 AI453185 diphtheria toxin receptor (heparin- 1.62 0.49 0.85 0.62 0.15 R45640 binding epidermal growth factor-like growth factor) vasoactive intestinal peptide receptor 1 2.31 0.43 0.31 0.23 0.54 H73241 Fc fragment of IgG, low affinity IIIb, 3.85 −0.20 0.26 0.76 0.02 H20822 receptor for (CD16) Fc fragment of IgG, low affinity IIb, 1.63 0.27 0.06 1.21 0.62 R68106 receptor for (CD32) Fc fragment of IgE, high affinity I, 1.78 0.43 0.00 0.56 0.84 AI676097 receptor for; alpha polypeptide leukocyte immunoglobulin-like 2.25 0.44 0.05 0.38 0.99 N63398 receptor, subfamily A leukocyte immunoglobulin-like 14.21 1.10 0.07 AI815229 receptor, subfamily B (with TM and ITIM domains), member 3 leukocyte immunoglobulin-like 2.31 0.75 0.43 0.19 0.40 AA076350 receptor, subfamily B (with TM and ITIM domains), member 4 leukocyte immunoglobulin-like 1.67 0.35 0.60 0.18 0.90 H54023 receptor, subfamily B peroxisome proliferative activated 1.18 0.38 0.85 0.87 0.26 AI739498 receptor, alpha protein tyrosine phosphatase, receptor 2.19 0.43 1.06 0.46 N49751 type, f polypeptide (PTPRF), interacting protein (liprin), α1 protein tyrosine phosphatase, receptor 1.55 0.44 0.64 0.30 0.81 H74265 type, C protein tyrosine phosphatase, receptor 2.08 0.23 0.37 0.56 0.48 AA464542 type, E protein tyrosine phosphatase, receptor 2.27 0.02 0.44 0.64 AA464590 type, N polypeptide 2 protein tyrosine phosphatase, receptor 2.34 0.11 0.43 0.24 0.89 AI924306 type, H protein tyrosine phosphatase, receptor- 1.59 0.63 0.34 0.72 0.35 AA476461 type, Z polypeptide 1 protein tyrosine phosphatase, non- 1.07 0.94 0.43 0.25 1.13 H03504 receptor type 21 MAP kinase 8 interacting protein 2 1.70 0.07 0.85 0.47 0.59 AA418293 MAP kinase kinase kinase 4 1.27 0.37 0.79 1.59 −5.28 AA402447 MAP kinase kinase kinase 14 1.00 0.34 0.66 2.10 1.49 W61116 MAP kinase 8 interacting protein 2 2.90 0.16 0.35 0.24 0.55 AI202738 MAP kinase kinase kinase 12 1.48 0.20 0.91 0.58 0.68 AA053674 MAP kinase kinase kinase kinase 3 2.21 0.45 0.20 1.03 0.41 AA043537 MAP kinase kinase kinase 6 2.62 0.37 0.38 0.70 AW084649 MAP kinase kinase kinase kinase 4 1.04 0.96 0.09 0.29 2.79 AA417711 MAP kinase kinase kinase 11 1.53 0.65 0.41 0.99 0.44 R80779 MAP kinase kinase kinase 10 1.32 1.23 0.27 0.50 0.76 H01340 MAP kinase 9 2.54 0.57 0.39 0.16 0.38 AA157286 MAP kinase kinase kinase 1 1.23 0.61 0.42 0.81 1.07 AI538525 MAP kinase kinase kinase 8 0.66 1.52 1.82 9.50 0.59 W56266 MAP kinase-activated protein kinase 3 0.52 2.13 2.68 1.13 1.93 W68281 MAP kinase kinase 2 0.84 1.20 3.35 0.02 1.31 AA425826 MAP kinase kinase kinase 7 1.00 0.97 1.62 7.46 AA460969 MAP kinase 7 0.09 11.45 11.80 33.43 H39192 MAP kinase kinase 6 0.10 17.83 9.61 32.30 H07920 regulator of G-protein signalling 5 3.7397 0.27 0.06 0.68 0.18 AA668470 regulator of G-protein signalling 13 1.8564 0.54 0.45 0.07 1.09 H70047 G protein-coupled receptor 1.04 1.84 0.16 0.09 0.96 R91916 G protein-coupled receptor 17 1.78 0.32 0.56 0.39 0.77 AI953187 G protein-coupled receptor kinase 7 2.62 0.34 0.91 0.38 AA488413 orphan seven-transmembrane receptor, 7.16 1.06 0.10 0.11 0.14 AI131555 chemokine related apoptosis antagonizing transcription 1.00 0.28 2.50 1.28 0.19 AI439571 factor caspase 1, apoptosis-related cysteine 2.83 0.44 0.33 0.35 T95052 protease (interleukin 1, beta, convertase) programmed cell death 8 (apoptosis- 1.00 1.07 0.35 1.94 0.08 AA496348 inducing factor)

TABLE 23 Pro-inflammatory polynucleotides up-regulated by peptide treatment of A549 cells. The cationic peptides at concentrations of 50 μg/ml were shown to increase the expression of certain pro-inflammatory polynucleotides (data is a subset of Table 21). Peptide was incubated with the human A549 epithelial cells for 4 h and the RNA was isolated, converted into labeled cDNA probes and hybridized to Human cDNA arrays ID#PRHU03-S3. The intensity of polynucleotides in unstimulated cells is shown in the second column. The “Ratio Peptide: Unstimulated” columns refers to the intensity of polynucleotide expression in peptide-simulated cells divided by the intensity of unstimulated cells. Unstim. Ratio Peptide: Unstimulated Accession Polynucleotide/Protein and function Intensity ID 2 ID 3 ID 19 ID 1 Number IL-11 Rα; Receptor for pro- 0.55 2.39 0.98 4.85 1.82 AA454657 inflammatory cytokine, inflammation IL-17 R; Receptor for IL-17, an inducer 0.54 2.05 1.97 1.52 1.86 AW029299 of cytokine production in epithelial cells small inducible cytokine subfamily A, 1.00 3.88 2.41 AI922341 member 21; a chemokine CD31; Leukocyte and cell to cell 0.59 2.71 3.13 1.01 1.68 R22412 adhesion (PECAM) CCR6; Receptor for chemokine MIP-3α 0.14 4.51 7.75 6.92 7.79 N57964 integrin, alpha 2 (CD49B, alpha 2 1.00 0.89 2.44 3.62 0.88 AA463257 subunit of VLA-2 receptor; Adhesion to leukocytes integrin, alpha 3 (antigen CD49C, alpha 0.94 0.79 2.51 1.88 1.07 AA424695 3 subunit of VLA-3 receptor); Leukocyte Adhesion integrin, alpha E; Adhesion 0.01 179.33 120.12 28.48 81.37 AA425451 integrin, beta 4; Leukocyte adhesion 0.65 0.79 2.17 4.94 1.55 AA485668 C-type lectin-like receptor-2; Leukocyte 0.45 2.09 7.92 2.24 5.29 H70491 adhesion

TABLE 24 Pro-inflammatory polynucleotides down-regulated by peptide treatment of A549 cells. The cationic peptides at concentrations of 50 μg/ml were shown to decrease the expression of certain pro-inflammatory polynucleotides (data is a subset of Table 22). Peptide was incubated with the human A549 epithelial cells for 4 h and the RNA was isolated, converted into labeled cDNA probes and hybridized to Human cDNA arrays ID#PRHU03-S3. The intensity of polynucleotides in unstimulated cells is shown in the second column. The “Ratio Peptide: Unstimulated” columns refers to the intensity of polynucleotide expression in peptide-simulated cells divided by the intensity of unstimulated cells. Unstim Ratio Peptide: Unstimulated Accession Polynucleotide/Protein; Function Intensity ID 2 ID 3 ID 19 ID 1 Number Toll-like receptor (TLR) 1; Response to gram 3.22 0.35 0.31 0.14 0.19 AI339155 positive bacteria TLR 2; Response to gram positive bacteria and 2.09 0.52 0.31 0.48 0.24 T57791 yeast TLR 5; May augment other TLR responses, 8.01 0.12 0.39 N41021 Responsive to flagellin TLR 7: Putative host defence mechanism 5.03 0.13 0.11 0.20 0.40 N30597 TNF receptor-associated factor 2; Inflammation 0.82 1.22 0.45 2.50 2.64 T55353 TNF receptor-associated factor 3; Inflammation 3.15 0.15 0.72 0.32 AA504259 TNF receptor superfamily, member 12; 4.17 0.59 0.24 0.02 W71984 Inflammation TNF R superfamily, member 17; Inflammation 2.62 0.38 0.55 0.34 AA987627 TRAF and TNF receptor-associated protein; 1.33 0.75 0.22 0.67 0.80 AA488650 TNF signalling small inducible cytokine subfamily A, member 2.26 0.32 0.44 1.26 AA495985 18; Chemokine small inducible cytokine subfamily A, member 2.22 0.19 0.38 0.45 0.90 AI285199 20; Chemokine small inducible cytokine subfamily A, member 2.64 0.38 0.31 1.53 AA916836 23; Chemokine small inducible cytokine subfamily B, member 3.57 0.11 0.06 0.28 0.38 AI889554 6 (granulocyte chemotactic protein); Chemokine small inducible cytokine subfamily B, member 2.02 0.50 1.07 0.29 0.40 AA878880 10; Chemokine small inducible cytokine A3 (homologous to 2.84 1.79 0.32 0.35 AA677522 mouse Mip-1α); Chemokine IL-12 receptor, beta 2; Interleukin and 4.58 0.67 0.22 AA977194 Interferon receptor IL-18 receptor 1; Induces IFN-γ 1.78 0.50 0.42 0.92 0.56 AA482489 selectin L (lymphocyte adhesion molecule 1); 4.43 0.03 0.23 0.61 H00662 Leukocyte adhesion vascular cell adhesion molecule 1; Leukocyte 1.40 0.20 0.72 0.77 0.40 H16591 adhesion intercellular adhesion molecule 3; Leukocyte 1.00 0.12 0.31 2.04 1.57 AA479188 adhesion integrin, alpha 1; Leukocyte adhesion 2.42 0.41 0.26 0.56 AA450324

TABLE 25 Anti-inflammatory polynucleotides up-regulated by peptide treatment of A549 cells. The cationic peptides at concentrations of 50 μg/ml were shown to increase the expression of certain anti-inflammatory polynucleotides (data is a subset of Table 21). Peptide was incubated with the human A549 epithelial cells for 4 h and the RNA was isolated, converted into labeled cDNA probes and hybridized to Human cDNA arrays ID#PRHU03-S3. The intensity of polynucleotides in unstimulated cells is shown in the second column. The “Ratio Peptide: Unstimulated” columns refers to the intensity of polynucleotide expression in peptide-simulated cells divided by the intensity of unstimulated cells. Unstim Ratio Peptide: Unstimulated Accession Polynucleotide/Protein; Function Intensity ID 2 ID 3 ID 19 ID 1 Number IL-1 R antagonist homolog 1; Inhibitor of septic 0.00 3085.96 1855.90 869.57 AI167887 shock IL-10 R beta; Receptor for cytokine synthesis 0.53 2.51 1.56 1.88 3.10 AA486393 inhibitor TNF R, member 1B; Apoptosis 0.28 17.09 3.01 14.93 3.60 AA150416 TNF R, member 5; Apoptosis (CD40L) 33.71 2.98 0.02 H98636 TNF R, member 11b; Apoptosis 1.00 5.29 4.50 0.78 AA194983 IK cytokine, down-regulator of HLA II; Inhibits 0.50 3.11 2.01 1.74 3.29 R39227 antigen presentation TGFB inducible early growth response 2; anti- 0.90 2.38 2.08 0.87 1.11 AI473938 inflammatory cytokine CD2; Adhesion molecule, binds LFAp3 1.00 2.62 0.87 1.15 0.88 AA927710

TABLE 26 Anti-inflammatory polynucleotides down-regulated by peptide treatment of A549 cells. The cationic peptides at concentrations of 50 μg/ml were shown to increase the expression of certain anti-inflammatory polynucleotides (data is a subset of Table 21). Peptide was incubated with the human A549 epithelial cells for 4 h and the RNA was isolated, converted into labeled cDNA probes and hybridized to Human cDNA arrays ID#PRHU03-S3. The intensity of polynucleotides in unstimulated cells is shown in the second column. The “Ratio Peptide: Unstimulated” columns refers to the intensity of polynucleotide expression in peptide-simulated cells divided by the intensity of unstimulated cells. Polynucleotide/Protein; Unstim Ratio Peptide: Unstimulated Accession Function Intensity ID 2 ID 3 ID 19 ID 1 Number MAP kinase 9 2.54 0.57 0.39 0.16 0.38 AA157286

TABLE 27 Polynucleotides up-regulated by SEQ ID NO: 6, in primary human macrophages. The peptide SEQ ID NO: 6 at a concentration of 50 μg/ml was shown to increase the expression of many polynucleotides. Peptide was incubated with the human macrophages for 4 h and the RNA was isolated, converted into labeled cDNA probes and hybridized to Human Operon arrays (PRHU04). The intensity of polynucleotides in unstimulated cells is shown in the second column. The “Ratio peptide treated: Control” columns refer to the intensity of polynucleotide expression in peptide- simulated cells divided by the intensity of unstimulated cells. Gene Control: Unstimulated Ratio peptide (Accession Number) cells treated: control proteoglycan 2 (Z26248) 0.69 9.3 Unknown (AK001843) 26.3 8.2 phosphorylase kinase alpha 1 (X73874) 0.65 7.1 actinin, alpha 3 (M86407) 0.93 6.9 DKFZP586B2420 protein (AL050143) 0.84 5.9 Unknown (AL109678) 0.55 5.6 transcription factor 21 (AF047419) 0.55 5.4 Unknown (A433612) 0.62 5.0 chromosome condensation 1-like (AF060219) 0.69 4.8 Unknown (AL137715) 0.66 4.4 apoptosis inhibitor 4 (U75285) 0.55 4.2 TERF1 (TRF1)-interacting nuclear factor 2 0.73 4.2 (NM_012461) LINE retrotransposable element 1 (M22333) 6.21 4.0 1-acylglycerol-3-phosphate O-acyltransferase 1 0.89 4.0 (U56417) Vacuolar proton-ATPase, subunit D; V- 1.74 4.0 ATPase, subunit D (X71490) KIAA0592 protein (AB011164) 0.70 4.0 potassium voltage-gated channel KQT-like 0.59 3.9 subfamily member 4 (AF105202) CDC14 homolog A (AF000367) 0.87 3.8 histone fold proteinCHRAC17 (AF070640) 0.63 3.8 Cryptochrome 1 (D83702) 0.69 3.8 pancreatic zymogen granule membrane 0.71 3.7 associated protein (AB035541) Sp3 transcription factor (X68560) 0.67 3.6 hypothetical protein FLJ20495 (AK000502) 0.67 3.5 E2F transcription factor 5, p130-binding 0.56 3.5 (U31556) hypothetical protein FLJ20070 (AK000077) 1.35 3.4 glycoprotein IX (X52997) 0.68 3.4 KIAA1013 protein (AB023230) 0.80 3.4 eukaryotic translation initiation factor 4A, 2.02 3.4 isoform 2 (AL137681) FYN-binding protein (AF198052) 1.04 3.3 guanine nucleotide binding protein, gamma 0.80 3.3 transducing activity polypeptide 1 (U41492) glypican 1 (X54232) 0.74 3.2 mucosal vascular addressin cell adhesion 0.65 3.2 molecule 1 (U43628) lymphocyte antigen (M38056) 0.70 3.2 H1 histone family, member 4 (M60748) 0.81 3.0 translational inhibitor protein p14.5 (X95384) 0.78 3.0 hypothetical protein FLJ20689 (AB032978) 1.03 2.9 KIAA1278 protein (AB03104) 0.80 2.9 unknown (AL031864) 0.95 2.9 chymotrypsin-like protease (X71877) 3.39 2.9 calumenin (NM_001219) 2.08 2.9 protein kinase, cAMP-dependent, regulatory, 7.16 2.9 type I, beta (M65066) POU domain, class 4, transcription factor 2 0.79 2.8 (U06233) POU domain, class 2, associating factor 1 1.09 2.8 (Z49194) KIAA0532 protein (AB011104) 0.84 2.8 unknown (AF068289) 1.01 2.8 unknown (AL117643) 0.86 2.7 cathepsin E (M84424) 15.33 2.7 matrix metalloproteinase 23A (AF056200) 0.73 2.7 interferon receptor 2 (L42243) 0.70 2.5 MAP kinase kinase 1 (L11284) 0.61 2.4 protein kinase C, alpha (X52479) 0.76 2.4 c-Cbl-interacting protein (AF230904) 0.95 2.4 c-fos induced growth factor (Y12864) 0.67 2.3 cyclin-dependent kinase inhibitor 1B (S76988) 0.89 2.2 zinc finger protein 266 (X78924) 1.67 2.2 MAP kinase 14 (L35263) 1.21 2.2 KIAA0922 protein (AB023139) 0.96 2.1 bone morphogenetic protein 1 (NM_006129) 1.10 2.1 NADH dehydrogenase 1 alpha subcomplex, 10 1.47 2.1 (AF087661) bone morphogenetic protein receptor, type IB 0.50 2.1 (U89326) interferon regulatory factor 2 (NM 002199) 1.46 2.0 protease, serine, 21 (AB031331) 0.89 2.0

TABLE 28 Polynucleotides down-regulated by SEQ ID NO: 6, in primary human macrophages. The peptide SEQ ID NO: 6 at a concentration of 50 μg/ml was shown to increase the expression of many polynucleotides. Peptide was incubated with the human macrophages for 4 h and the RNA was isolated, converted into labeled cDNA probes and hybridized to Human Operon arrays (PRHU04). The intensity of polynucleotides in ustimulated cells is shown in the second column. The “Ratio of Peptide:Control” columns refers to the intensity of polynucleotides expressions in peptide- stimulated cells divided by the intensity of unstimulated cells. Control: Unstimulated Ratio peptide Gene (Accession Number) cells treated:control Unknown (AL049263) 17 0.06 integrin-linked kinase (U40282) 2.0 0.13 KIAA0842 protein (AB020649) 1.1 0.13 Unknown (AB037838) 13 0.14 Granulin (AF055008) 8.6 0.14 glutathione peroxidase 3 (NM_002084) 1.2 0.15 KIAA0152 gene product (D63486) 0.9 0.17 TGFB1-induced anti-apoptotic 0.9 0.19 factor 1 (D86970) disintegrin protease (Y13323) 1.5 0.21 proteasome subunit 0.7 0.22 beta type 7 (D38048) cofactor required for Sp1 0.9 0.23 transcriptional activation subunit 3 (AB033042) TNF receptor superfamily, 0.8 0.26 member 14 (U81232) proteasome 26S subunit 1.1 0.28 non-ATPase 8 (D38047) proteasome subunit 0.7 0.29 beta type, 4 (D26600) TNF receptor superfamily 1.7 0.29 member 1B (M32315) cytochrome c oxidase 3.3 0.30 subunit Vic (X13238) S100 calcium-binding 3.8 0.31 protein A4 (M80563) proteasome subunit alpha 2.9 0.31 type, 6 (X59417) proteasome 26S subunit 1.0 0.32 non-ATPase, 10 (AL031177) MAP kinase kinase 0.8 0.32 kinase 2 (NM_006609) ribosomal protein 5.5 0.32 L11 (X79234) matrix metalloproteinase 1.0 0.32 14 (Z48481) proteasome subunit beta type, 1.5 0.33 5 (D29011) MAP kinase-activated protein 1.5 0.34 kinase 2 (U12779) caspase 3 (U13737) 0.5 0.35 jun D proto-oncogene (X56681) 3.0 0.35 proteasome 26S subunit, 1.3 0.35 ATPase, 3 (M34079) IL-1 receptor-like 0.7 0.35 1 (AB012701) interferon alpha-inducible 13 0.35 protein (AB019565) SDF receptor 1 (NM_012428) 1.6 0.35 Cathepsin D (M63138) 46 0.36 MAP kinase kinase 3 (D87116) 7.4 0.37 TGF, beta-induced, (M77349) 1.8 0.37 TNF receptor superfamily, 1.1 0.37 member 10b (AF016266) proteasome subunit beta type, 1.3 0.38 6 (M34079) nuclear receptor binding 5.2 0.38 protein (NM_013392) Unknown (AL050370) 1.3 0.38 protease inhibitor 1 0.7 0.40 alpha-1-antitrypsin (X01683) proteasome subunit alpha type, 5.6 0.40 7 (AF054185) LPS-induced TNF-alpha 5.3 0.41 factor (NM_004862) transferrin receptor (X01060) 14 0.42 proteasome 26S subunit 1.8 0.44 non-ATPase 13 (AB009398) MAP kinase kinase 5 (U25265) 1.3 0.44 Cathepsin L(X12451) 15 0.44 IL-1 receptor-associated 1.7 0.45 kinase 1 (L76191) MAP kinase kinase kinase 1.1 0.46 kinase 2 (U07349) peroxisome proliferative 2.2 0.46 activated receptor delta (AL022721) TNF superfamily, 16 0.46 member 15 (AF039390) defender against cell 3.9 0.46 death 1 (D15057) TNF superfamily member 287 0.46 10 (U37518) cathepsin H (X16832) 14 0.47 protease inhibitor 12 (Z81326) 0.6 0.48 proteasome subunit alpha type, 2.6 0.49 4 (D00763) proteasome 26S subunit ATPase, 1.8 0.49 1 (L02426) proteasome 26S subunit ATPase, 2.1 0.49 2 (D11094) caspase 7 (U67319) 2.4 0.49 matrix metalloproteinase 2.5 0.49 7 (Z11887)

TABLE 29 Polynucleotides up-regulated by SEQ ID NO: 1, in HBE cells. The Peptide SEQ ID NO: 1 at a concentration of 50 μg/ml was shown to increase the expression of many polynucleotides. Peptide was incubated with the human HBE epithelial cells for 4 h and the RNA was isolated, converted into labeled cDNA probes and hybridized to Human Operon arrays (PRHU04). The intensity of polynucleotides in unstimulated cells is shown in the second column. The “Ratio Peptide:Control” columns refer to the intensity of polynucleotide expression in peptide-simulated cells divided by the intensity of unstimulated cells. Control: Accession Unstimulated Ratio peptide Number Gene cells treated:control AL110161 Unknown 0.22 5218.3 AF131842 Unknown 0.01 573.1 AJ000730 solute carrier family 0.01 282.0 Z25884 chloride channel 1 0.01 256.2 M93426 protein tyrosine phosphatase 0.01 248.7 receptor-type, zeta X65857 olfactory receptor, family 1, 0.01 228.7 subfamily D, member 2 M55654 TATA box binding protein 0.21 81.9 AK001411 hypothetical protein 0.19 56.1 D29643 dolichyl-diphosphooligosaccharide- 1.56 55.4 protein glycosyltransferase AF006822 myelin transcription factor 2 0.07 55.3 AL117601 Unknown 0.05 53.8 AL117629 DKFZP434C245 protein 0.38 45.8 M59465 tumor necrosis factor, 0.50 45.1 alpha-induced protein 3 AB013456 aquaporin 8 0.06 41.3 AJ131244 SEC24 related gene family, 0.56 25.1 member A AL110179 Unknown 0.87 24.8 AB037844 Unknwon 1.47 20.6 Z47727 polymerase II polypeptide K 0.11 20.5 AL035694 Unknown 0.81 20.4 X68994 H.sapiens CREB gene 0.13 19.3 AJ238379 hypothetical protein 1.39 18.5 NM_003519 H2B histone family member 0.13 18.3 U16126 glutamate receptor, ionotropic 0.13 17.9 kainate 2 U29926 adenosine monophosphate 0.16 16.3 deaminase AK001160 hypothetical protein 0.39 14.4 U18018 ets variant gene 4 0.21 12.9 D80006 KIAA0184 protein 0.21 12.6 AK000768 hypothetical protein 0.30 12.3 X99894 insulin promoter factor 1, 0.26 12.0 AL031177 Unknown 1.09 11.2 AF052091 unknown 0.28 10.9 L38928 5, 10-methenyltetrahydrofolate 0.22 10.6 synthetase AL117421 unknown 0.89 10.1 AL133606 hypothetical protein 0.89 9.8 NM_016227 membrane protein CH1 0.28 9.6 NM_006594 adaptor-related protein 0.39 9.3 complex 4 U54996 ZW10 homolog, protein 0.59 9.3 AJ007557 potassium channel, 0.28 9.0 AF043938 muscle RAS oncogene 1.24 8.8 AK001607 unknown 2.74 8.7 AL031320 peroxisomal biogenesis 0.31 8.4 factor 3 D38024 unknown 0.31 8.3 AF059575 LIM homeobox TF 2.08 8.2 AF043724 hepatitis A virus cellular 0.39 8.1 receptor 1 AK002062 hypothetical protein 2.03 8.0 L13436 natriuretic peptide receptor 0.53 7.8 U33749 thyroid transcription factor 1 0.36 7.6 AF011792 cell cycle progression 2 protein 0.31 7.6 AK000193 hypothetical protein 1.18 6.8 AF039022 exportin, tRNA 0.35 6.8 M17017 interleukin 8 0.50 6.7 AF044958 NADH dehydrogenase 0.97 6.5 U35246 vacuolar protein sorting 0.48 6.5 AK001326 tetraspan 3 1.59 6.5 M55422 Krueppel-related zinc 0.34 6.4 finger protein U44772 palmitoyl-protein 1.17 6.3 thioesterase AL117485 hypothetical protein 0.67 5.9 AB037776 unknown 0.75 5.7 AF131827 unknown 0.69 5.6 AL137560 unknown 0.48 5.2 X05908 annexin A1 0.81 5.1 X68264 melanoma adhesion molecule 0.64 5.0 AL161995 neurturin 0.86 4.9 AF037372 cytochrome c oxidase 0.48 4.8 NM_016187 bridging integrator 2 0.65 4.8 AL137758 unknown 0.57 4.8 U59863 TRAF family member-associated 0.46 4.7 NFKB activator Z30643 chloride channel Ka 0.70 4.7 D16294 acetyl-Coenzyme A 1.07 4.6 acyltransferase 2 AJ132592 zinc finger protein 281 0.55 4.6 X82324 POU domain TF 1.73 4.5 NM_016047 CGI-110 protein 1.95 4.5 AK001371 hypothetical protein 0.49 4.5 M60746 H3 histone family member D 3.05 4.5 AB033071 hypothetical protein 4.47 4.4 AB002305 KIAA0307 gene product 1.37 4.4 X92689 UDP-N-acetyl-alpha-D- 0.99 4.4 galactosamine: polypeptide N- acetylgalactosaminyltransferase 3 AL049543 glutathione peroxidase 5 1.62 4.3 U43148 patched homolog 0.96 4.3 M67439 dopamine receptor D5 2.61 4.2 U09850 zinc finger protein 143 0.56 4.2 L20316 glucagon receptor 0.75 4.2 AB037767 a disintegrin-like and 0.69 4.2 metalloprotease NM_017433 myosin IIIA 99.20 4.2 D26579 a disintegrin and 0.59 4.1 metalloprotease domain 8 L10333 reticulon 1 1.81 4.1 AK000761 unknown 1.87 4.1 U91540 NK homeobox family 3, A 0.80 4.1 Z17227 interleukin 10 receptor, beta 0.75 4.0

TABLE 30 Polynucleotides down-regulated by Peptide (50 μg/ml), SEQ ID NO: 1, in HBE cells. The Peptide SEQ ID: 1 at a concentration of 50 μg/ml was shown to decrease the expression of many polynucleotides. Peptide was incubated with the human A549 epithelial cells for 4 h and the RNA was isolated, converted into labeled cDNA probes and hybridized to Human Operon arrays (PRHU04). The intensity of polynucleotides in unstimulated cells is shown in the third column. The “Ratio Peptide:Control” columns refer to the intensity of polynucleotide expression in peptide-simulated cells divided by the intensity of unstimulated cells. Control: Ratio of SEQ Accession Unstimulated ID NO: 1- Number Gene Cells treated:control AC004908 Unknown 32.4 0.09 S70622 G1 phase-specific gene 43.1 0.10 Z97056 DEAD/H box polypeptide 12.8 0.11 AK002056 hypothetical protein 11.4 0.12 L33930 CD24 antigen 28.7 0.13 X77584 thioredoxin 11.7 0.13 NM_014106 PRO1914 protein 25.0 0.14 M37583 H2A histone family member 22.2 0.14 U89387 polymerase (RNA) II 10.2 0.14 polypeptide D D25274 ras-related C3 botulinum 10.3 0.15 toxin substrate 1 J04173 phosphoglycerate mutase 1 11.4 0.15 U19765 zinc finger protein 9 8.9 0.16 X67951 proliferation-associated 14.1 0.16 gene A AL096719 profilin 2 20.0 0.16 AF165217 tropomodulin 4 14.6 0.16 NM_014341 mitochondrial carrier 11.1 0.16 homolog 1 AL022068 Unknown 73.6 0.17 X69150 ribosomal protein S18 42.8 0.17 AL031577 Unknown 35.0 0.17 AL031281 Unknown 8.9 0.17 AF090094 Human mRNA for ornithine 10.3 0.17 decarboxylase antizyme, AL022723 HLA-G histocompatibility 20.6 0.18 antigen, class I, G U09813 ATP synthase, H+ 9.8 0.18 transporting mitochondrial F0 complex AF000560 Homo sapiens TTF-I 20.2 0.19 interacting peptide 20 NM_016094 HSPC042 protein 67.2 0.19 AF047183 NADH dehydrogenase 7.5 0.19 D14662 anti-oxidant protein 2 8.1 0.19 (non-selenium glutathione peroxidase, acidic calcium- independent phospholipas X16662 annexin A8 8.5 0.19 U14588 paxillin 11.3 0.19 AL117654 DKFZP586D0624 protein 12.6 0.20 AK001962 hypothetical protein 7.7 0.20 L41559 6-pyruvoyl-tetrahydropterin 9.1 0.20 synthase/dimerization cofactor of hepatocyte nuclear factor 1 alpha NM_016139 16.7Kd protein 21.0 0.21 NM_016080 CGI-150 protein 10.7 0.21 U86782 26S proteasome-associated 6.7 0.21 pad1 homolog AJ400717 tumor protein, 9.8 0.21 translationally- controlled 1 X07495 homeo box C4 31.0 0.21 AL034410 Unknown 7.3 0.22 X14787 thrombospondin 1 26.2 0.22 AF081192 purine-rich element 6.8 0.22 binding protein B D49489 protein disulfide isomerase- 11.0 0.22 related protein NM_014051 PTD011 protein 9.3 0.22 AK001536 Unknown 98.0 0.22 X62534 high-mobility group 9.5 0.22 protein 2 AJ005259 endothelial differentiation- 6.7 0.22 related factor 1 NM_000120 epoxide hydrolase 1, 10.0 0.22 microsomal M38591 S100 calcium-binding 23.9 0.23 protein A10 AF071596 immediate early response 3 11.5 0.23 X16396 methylene tetrahydrofolate 8.3 0.23 dehydrogenase AK000934 ATPase inhibitor precursor 7.6 0.23 AL117612 Unknown 10.7 0.23 AP119043 transcriptional intermediary 7.3 0.23 factor 1 gamma AF037066 solute carrier family 22 7.6 0.23 member 1-like antisense AF134406 cytochrome c oxidase 13.3 0.23 subunit AE000661 Unknown 9.2 0.24 AL157424 synaptojanin 2 7.2 0.24 X56468 tyrosine 3-monooxygenase/ 7.2 0.24 tryptophan 5-monooxygenase activation protein, U39318 ubiquitin-conjugating 10.7 0.24 enzyme E2D 3 AL034348 Unknown 24.4 0.24 D26600 proteasome subunit beta 11.4 0.24 type 4 AB032987 Unknown 16.7 0.24 J04182 lysosomal-associated 7.4 0.24 membrane protein 1 X78925 zinc finger protein 267 16.1 0.25 NM_000805 gastrin 38.1 0.25 U29700 anti-Mullerian hormone 12.0 0.25 receptor, type II Z98200 Unknown 13.4 0.25 U07857 signal recognition particle 10.3 0.25 L05096 Homo sapiens ribosomal 25.3 0.25 protein L39 AK001443 hypothetical protein 7.5 0.25 K03515 glucose phosphate isomerase 6.2 0.25 X57352 interferon induced 7.5 0.26 transmembrane protein 3 J02883 colipase pancreatic 5.7 0.26 M24069 cold shock domain protein 6.3 0.26 AJ269537 chondroitin-4- 60.5 0.26 sulfotransferase AL137555 Unknown 8.5 0.26 U89505 RNA binding motif 5.5 0.26 protein 4 U82938 CD27-binding protein 7.5 0.26 X99584 SMT3 homolog 1 12.8 0.26 AK000847 Unknown 35.8 0.27 NM_014463 Lsm3 protein 7.8 0.27 AL133645 Unknown 50.8 0.27 X78924 zinc finger protein 266 13.6 0.27 NM_004304 anaplastic lymphoma kinase 15.0 0.27 X57958 ribosomal protein L7 27.9 0.27 U63542 Unknown 12.3 0.27 AK000086 hypothetical protein 8.3 0.27 X57138 H2A histone family member N 32.0 0.27 AB023206 KIAA0989 protein 6.5 0.27 AB021641 gonadotropin inducible 5.5 0.28 transcriptn represser-1, AF050639 NADH dehydrogenase 5.5 0.28 M62505 complement component 5 7.5 0.28 receptor 1 X64364 basigin 5.8 0.28 AJ224082 Unknown 22.5 0.28 AF042165 cytochrome c oxidase 20.4 0.28 AK001472 anillin 10.9 0.28 X86428 protein phosphatase 12.7 0.28 2A subunit AF227132 candidate taste 5.1 0.28 receptor T2R5 Z98751 Unknown 5.3 0.28 D21260 clathrin heavy polypeptide 8.3 0.28 AF041474 actin-like 6 15.1 0.28 NM_005258 GTP cyclohydrolase I protein 7.6 0.28 L20859 solute carrier family 20 9.6 0.29 Z80783 H2B histone family member 9.0 0.29 AB011105 laminin alpha 5 7.1 0.29 AL008726 protective protein for 5.2 0.29 beta-galactosidase D29012 proteasome subunit 12.6 0.29 X63629 cadherin 3 P-cadherin 6.8 0.29 X02419 plasminogen activator 12.9 0.29 urokinase X13238 cytochrome c oxidase 8.0 0.29 X59798 cyclin D1 12.7 0.30 D78151 proteasome 26S subunit 7.6 0.31 AF054185 proteasome subunit 18.8 0.31 J03890 surfactant pulmonary- 5.5 0.32 associated protein C M34079 proteasome 26S subunit, 5.2 0.33

TABLE 31 Up-regulation of Polynucleotide expression in A549 cells induced by Formula A Peptides. The peptides at a concentration of 50 μg/ml were shown to increase the expression of many polynucleotides. Peptide was incubated with the human A549 epithelial cells for 4 h and the RNA was isolated, converted into labeled cDNA probes and hybridized to Human Operon arrays (PRHU04). The intensity of polynucleotides in control, unstimulated cells are shown in the second and third columns for labeling of cDNA with the dyes Cy3 and Cy5 respectively. The “ID#: Control” columns refer to the intensity of polynucleotide expression in peptide-simulated cells divided by the intensity of unstimulated cells. Accession control- control- ID 5: ID 6: ID 7: ID 8: ID 9: ID 10: Number Gene Cy3 Cy5 control control control control control control U12472 glutathione S- 0.09 0.31 13.0 3.5 4.5 7.0 4.3 16.4 transferase X66403 cholinergic 0.17 0.19 7.8 9.9 6.0 6.4 5.0 15.7 receptor AK001932 unknown 0.11 0.25 19.4 4.6 9.9 7.6 8.1 14.5 X58079 S100 calcium- 0.14 0.24 12.2 7.6 8.1 4.3 4.5 13.2 binding protein U18244 solute carrier 0.19 0.20 6.1 9.7 11.9 5.0 3.7 10.6 family 1 U20648 zinc finger 0.16 0.13 5.3 6.2 5.6 3.1 6.8 9.5 protein AB037832 unknown 0.10 0.29 9.0 4.2 9.4 3.1 2.6 8.7 AC002542 unknown 0.15 0.07 10.5 15.7 7.8 10.1 11.7 8.2 M89796 membrane- 0.15 0.14 2.6 6.1 7.6 3.5 13.3 8.1 spanning 4- domains, subfamily A AF042163 cytochrome c 0.09 0.19 3.9 3.2 7.6 6.3 4.9 7.9 oxidase AL032821 Vanin 2 0.41 0.23 2.5 5.2 3.2 2.1 4.0 7.9 U25341 melatonin 0.04 0.24 33.1 5.1 23.3 6.6 4.1 7.6 receptor 1B U52219 G protein- 0.28 0.20 2.1 6.2 6.9 2.4 3.9 7.1 coupled receptor X04506 apolipoprotein B 0.29 0.32 7.9 3.4 3.3 4.8 2.6 7.0 AB011138 ATPase type IV 0.12 0.07 3.5 12.9 6.6 6.4 21.3 6.9 AF055018 unknown 0.28 0.22 3.8 6.9 5.0 2.3 3.1 6.8 AK002037 hypothetical 0.08 0.08 2.9 7.9 14.1 7.9 20.1 6.5 protein AK001024 guanine 0.16 0.11 7.7 11.9 5.0 10.3 6.0 6.3 nucleotide- binding protein AF240467 TLR-7 0.11 0.10 20.4 9.0 3.4 9.4 12.9 6.1 AF105367 glucagon-like 0.15 0.35 23.2 2.6 3.0 10.6 2.9 5.7 peptide 2 receptor AL009183 TNFR 0.46 0.19 10.6 4.7 3.7 2.8 6.5 5.7 superfamily, member 9 X54380 pregnancy-zone 0.23 0.08 4.7 11.9 7.2 12.7 3.8 5.5 protein AL137736 unknown 0.22 0.15 2.1 7.2 3.3 7.1 4.6 5.5 X05615 thyroglobulin 0.28 0.42 6.3 2.7 7.7 2.4 3.1 5.4 D28114 myelin- 0.24 0.08 2.5 15.9 13.0 7.1 13.7 5.4 associated protein AK000358 microfibrillar- 0.28 0.28 8.7 4.2 7.2 3.2 2.4 5.3 associated protein 3 AK001351 unknown 0.12 0.22 3.9 7.6 8.7 3.9 2.3 5.2 U79289 unknown 0.14 0.27 2.5 2.7 2.8 2.0 4.3 5.1 AB014546 ring finger 0.12 0.34 6.8 2.4 4.1 2.7 2.0 5.0 protein AL117428 DKFZP434A236 0.10 0.07 2.8 16.1 12.8 9.7 14.2 4.9 protein AL050378 unknown 0.41 0.14 3.5 8.7 11.7 3.5 7.0 4.9 AJ250562 transmembrane 0.13 0.10 5.2 5.7 14.2 3.8 10.3 4.8 4 superfamily member 2 NM_001756 corticosteroid 0.28 0.13 4.0 7.9 6.5 14.9 5.6 4.8 binding globulin AL137471 hypothetical 0.29 0.05 3.7 18.0 6.2 7.2 16.3 4.7 protein M19684 protease 0.41 0.14 3.5 4.6 5.4 2.8 9.4 4.7 inhibitor 1 NM_001963 epidermal 0.57 0.05 3.4 6.2 1.8 32.9 14.7 4.4 growth factor NM_000910 neuropeptide Y 0.62 0.36 3.1 2.7 2.3 2.6 3.1 4.4 receptor AF022212 Rho GTPase 0.19 0.02 9.0 45.7 25.6 12.4 72.2 4.4 activating protein 6 AK001674 cofactor required 0.11 0.13 8.4 6.5 7.9 4.5 7.4 4.3 for Sp1 U51920 signal 0.23 0.27 3.4 3.8 2.1 4.1 8.8 4.2 recognition particle AK000576 hypothetical 0.27 0.06 4.4 14.7 7.4 14.1 8.6 4.2 protein AL080073 unknown 0.17 0.20 21.6 3.9 4.3 8.8 2.6 4.1 U59628 paired box gene 9 0.34 0.06 3.4 14.1 5.4 7.9 4.9 4.1 U90548 butyrophilin, 0.41 0.31 2.3 4.7 5.5 6.8 3.4 4.1 subfamily 3, member A3 M19673 cystatin SA 0.43 0.26 2.3 8.5 4.5 2.5 4.1 3.8 AL161972 ICAM 2 0.44 0.37 2.0 3.6 2.0 2.7 5.5 3.8 X54938 inositol 1,4,5- 0.32 0.22 3.9 3.3 6.2 3.1 4.4 3.7 trisphosphate 3- kinase A AB014575 KIAA0675 gene 0.04 0.13 46.2 4.5 10.2 8.0 6.2 3.4 product M83664 MHC II, DP beta 1 0.57 0.29 2.9 2.1 2.0 3.1 6.6 3.4 AK000043 hypothetical 0.34 0.14 2.7 7.1 3.7 9.4 8.8 3.3 protein U60666 testis specific 0.21 0.11 9.9 9.0 4.1 5.5 13.0 3.3 leucine rich repeat protein AK000337 hypothetical 0.49 0.19 4.3 5.1 4.7 10.6 7.1 3.3 protein AF050198 putative 0.34 0.15 7.0 6.3 3.6 5.6 11.9 3.3 mitochondrial space protein AJ251029 odorant-binding 0.28 0.12 4.4 9.4 7.2 8.8 7.1 3.2 protein 2A X74142 forkhead box 0.12 0.33 19.5 4.5 8.4 6.4 4.4 3.2 G1B AB029033 KIAA1110 0.35 0.24 3.1 2.2 5.6 5.2 3.1 3.1 protein D85606 cholecystokinin 0.51 0.14 4.3 3.9 4.6 3.5 7.2 3.1 A receptor X84195 acylphosphatase 0.32 0.19 4.8 3.7 5.0 11.2 9.8 3.0 2 muscle type U57971 ATPase Ca++ 0.29 0.13 2.2 7.9 1.8 6.3 4.8 3.0 transporting plasma membrane 3 J02611 apolipoprotein D 0.28 0.10 2.8 11.0 3.7 10.3 8.4 3.0 AF071510 lecithin retinol 0.07 0.05 7.9 3.8 11.7 46.0 16.3 3.0 acyltransferase AF131757 unknown 0.10 0.08 4.8 9.0 44.3 9.3 10.7 3.0 L10717 IL2-inducible T- 0.45 0.21 2.5 4.9 2.8 10.9 4.5 2.9 cell kinase L32961 4-aminobutyrate 0.64 0.32 3.6 2.9 3.2 5.3 2.3 2.9 aminotransferase NM_003631 poly (ADP- 0.46 0.41 9.7 3.9 4.1 3.8 2.8 2.7 ribose) glycohydrolase AF098484 pronapsin A 0.28 0.14 3.7 3.7 5.6 11.6 3.7 2.5 NM_009589 arylsulfatase D 0.73 0.16 3.2 5.6 6.0 48.6 7.2 2.4 M14764 TNFR 0.49 0.15 2.3 3.5 10.6 13.6 6.8 2.2 superfamily, member 16 AL035250 endothelin 3 0.52 0.14 2.1 7.3 4.8 4.5 3.7 2.2 M97925 defensin, alpha 0.33 0.07 4.0 14.7 7.8 9.4 3.5 2.1 5, Paneth cell- specific D43945 transcription 0.46 0.19 6.6 2.9 8.2 4.0 3.5 2.1 factor EC D16583 histidine 0.46 0.09 3.2 13.8 4.2 8.8 13.7 2.1 decarboxylase

TABLE 32 Up-regulation of Polynucleotide expression in A549 cells induced by Formula B Peptides. The peptides at a concentration of 50 μg/ml were shown to increase the expression of many polynucleotides. Peptide was incubated with the human A549 epithelial cells for 4 h and the RNA was isolated, converted into labeled cDNA probes and hybridized to Human Operon arrays (PRHU04). The intensity of polynucleotides in control, unstimulated cells are shown in the second and third columns for labeling of cDNA with the dyes Cy3 and Cy5 respectively. The “ID#: Control” columns refer to the intensity of polynucleotide expression in peptide-simulated cells divided by the intensity of unstimulated cells. Accession control- control- ID 12: ID 13: ID 14: ID 15: ID 16: ID 17: Number Gene Cy3 Cy5 control control control control control control AL157466 unknown 0.05 0.06 18.0 21.4 16.7 5.2 6.8 8.6 AB023215 KIAA0998 protein 0.19 0.07 14.8 10.6 7.9 14.4 6.6 16.1 AL031121 unknown 0.24 0.09 14.1 5.7 3.8 5.5 2.8 4.6 NM_016331 zinc finger protein 0.16 0.08 12.8 7.2 11.0 5.3 11.2 9.7 M14565 cytochrome P450 0.16 0.12 10.6 12.5 5.0 3.6 10.1 6.3 U22492 G protein-coupled receptor 8 0.28 0.07 10.4 8.9 4.8 10.8 6.6 3.6 U76010 solute carrier family 30 0.14 0.07 9.7 18.6 3.7 4.8 5.6 8.9 AK000685 unknown 0.51 0.10 9.0 3.1 2.8 3.9 15.3 3.0 AF013620 Immunoglobulin heavy variable 4-4 0.19 0.18 8.5 2.6 6.2 5.7 8.2 3.8 AL049296 unknown 0.61 0.89 8.1 3.2 2.7 3.2 2.7 2.0 AB006622 KIAA0284 protein 0.47 0.28 7.5 5.0 2.8 11.1 5.5 4.6 X04391 CD5 antigen 0.22 0.13 7.2 16.7 2.7 7.7 6.1 5.9 AK000067 hypothetical protein 0.80 0.35 7.1 4.6 2.1 3.2 8.5 2.2 AF053712 TNF superfamily_member 11 0.17 0.08 6.9 17.7 3.0 6.2 12.3 5.2 X58079 S100 calcium-binding protein A1 0.14 0.24 6.7 6.7 5.9 6.5 5.3 2.5 M91036 hemoglobin_gamma A 0.48 0.36 6.7 14.2 2.1 2.9 2.7 4.8 AF055018 unknown 0.28 0.22 6.3 10.7 2.7 2.6 4.6 6.5 L17325 pre-T/NK cell associated protein 0.19 0.29 6.1 4.4 6.5 4.7 4.0 4.0 D45399 phosphodiesterase 0.21 0.18 6.1 4.6 5.0 2.8 10.8 4.0 AB023188 KIAA0971 protein 0.29 0.13 5.9 10.6 3.6 3.4 10.6 7.2 NM_012177 F-box protein 0.26 0.31 5.9 5.5 3.8 2.8 3.0 6.8 D38550 E2F TF 3 0.43 0.39 5.8 3.4 2.1 4.5 2.5 2.4 AL050219 unknown 0.26 0.04 5.7 17.0 3.1 9.2 30.3 16.1 AL137540 unknown 0.67 0.79 5.5 3.2 3.9 10.9 2.9 2.3 D50926 KIAA0136 protein 0.57 0.21 5,4 5.6 2.0 3.3 4.4 3.2 AL137658 unknown 0.31 0.07 5.4 12.1 2.6 10.8 3.9 8.6 U21931 fructose-bisphosphatase 1 0.48 0.14 5.4 4.1 2.9 3.6 6.0 3.2 AK001230 DKFZP586D211 protein 0.43 0.26 5.0 4.6 2.1 2.2 2.5 2.7 AL137728 unknown 0.67 0.47 5.0 5.9 2.2 6.8 5.9 2.1 AB022847 unknown 0.39 0.24 4.5 2.2 3.5 4.3 3.8 3.7 X75311 mevalonate kinase 0.67 0.22 4.3 4.0 2.0 8.3 4.0 5.1 AK000946 DKFZP566C243 protein 0.36 0.29 4.1 3.8 3.9 5.4 25.8 2.7 AB023197 KIAA0980 protein 0.25 0.30 4.0 8.3 2.1 8.8 2.2 4.9 AB014615 fibroblast growth factor 8 0.19 0.07 3.9 3.3 7.0 3.4 2.2 7.7 X04014 unknown 0.29 0.16 3.8 2.5 2.2 3.0 5.5 3.1 U76368 solute carrier family 7 0.46 0.17 3.8 3.8 2.8 3.2 4.2 3.0 AB032436 unknown 0.14 0.21 3.8 2.7 6.1 3.2 4.5 2.6 AB020683 KIAA0876 protein 0.37 0.21 3.7 4.2 2.2 5.3 2.9 9.4 NM_012126 carbohydrate sulfotransferase 5 0.31 0.20 3.7 5.2 3.2 3.4 3.9 2.5 AK002037 hypothetical protein 0.08 0.08 3.7 17.1 4.6 12.3 11.0 8.7 X78712 glycerol kinase pseudogene 2 0.17 0.19 3.6 2.5 4.5 5.3 2.2 3.3 NM_014178 HSPC156 protein 0.23 0.12 3.5 8.4 2.9 6.9 14.4 5.5 AC004079 homeo box A2 0.31 0.11 3.5 7.0 2.1 2.0 7.3 9.1 AL080182 unknown 0.51 0.21 3.4 3.5 2.2 2.1 2.9 2.4 M91036 hemoglobin gamma G 0.22 0.02 3.4 26.3 5.8 6.8 30.4 21.6 AJ000512 serum/glucocorticoid regulated 0.27 0.43 3.3 2.1 4.9 2.3 3.9 2.7 kinase AK002140 hypothetical protein 0.28 0.14 3.3 9.9 2.8 2.1 16.6 7.2 AL137284 unknown 0.22 0.04 3.3 7.2 4.1 6.0 12.2 3.7 Z11898 POU domain_class 5 TF 1 0.12 0.29 3.2 3.7 8.2 2.5 6.6 2.2 AB017016 brain-specific protein 0.27 0.29 3.1 2.8 2.5 2.8 3.3 5.5 X54673 Solute-carrier family 6 0.34 0.08 2.9 12.0 2.2 10.4 7.4 5.9 AL033377 unknown 0.40 0.22 2.6 2.6 2.6 2.3 4.5 2.2 X85740 CCR4 0.34 0.05 2.6 2.3 2.6 2.5 12.5 5.2 AB010419 core-binding factor 0.59 0.20 2.5 12.8 2.0 2.8 2.9 5.9 AL109726 uknown 0.14 0.15 2.3 9.0 4.3 4.4 2.6 3.7 NM_012450 sulfate transporter 1 0.15 0.10 2.2 3.1 8.2 9.9 4.7 5.9 J04599 biglycan 0.39 0.30 2.1 3.3 6.6 2.2 2.7 5.4 AK000266 hypothetical protein 0.49 0.35 2.1 3.5 3.5 6.6 4.3 4.0

TABLE 33 Up-regulation of Polynucleotide expression in A549 cells induced by Formula C Peptides. The peptides at a concentration of 50 μg/ml were shown to increase the expression of many polynucleotides. Peptide was incubated with the human A549 epithelial cells for 4 h and the RNA was isolated, converted into labeled cDNA probes and hybridized to Human Operon arrays (PRHU04). The intensity of polynucleotides in control, unstimulated cells are shown in the second and third columns for labeling of cDNA with the dyes Cy3 and Cy5 respectively. The “ID#: Control” columns refer to the intensity of polynucleotide expression in peptide-simulated cells divided by the intensity of unstimulated cells. Accession control- control- ID 19: ID 20: ID 21: ID 22: ID 23: ID 24: Number Gene Cy3 Cy5 control control control control control control NM_014139 sodium channel voltage-gated, 0.04 0.05 31.6 25.2 18.0 9.7 22.2 11.2 X84003 TATA box binding protein 0.47 0.07 31.8 12.7 2.5 2.8 18.0 14.2 AF144412 lens epithelial cell protein 0.25 0.07 23.9 8.0 6.8 3.4 16.2 3.5 AL080107 unknown 0.11 0.06 17.8 34.4 12.4 6.2 5.4 7.9 AF052116 unknown 0.34 0.07 15.5 3.9 9.2 3.0 6.9 2.7 AB033063 unknown 0.46 0.13 15.2 10.3 4.0 2.6 7.2 11.2 AK000258 hypothetical protein 0.27 0.07 13.9 8.0 3.5 3.4 26.5 11.5 NM_006963 zinc finger protein 0.10 0.08 12.8 6.8 6.2 5.9 17.2 1241.2 NM_014099 PRO1768 protein 0.30 0.06 12.3 17.4 5.4 5.4 19.5 3.4 AK000996 hypothetical protein 0.17 0.07 10.0 8.0 9.7 7.4 20.7 16.3 M81933 cell division cycle 25A 0.13 0.21 8.8 7.8 19.6 15.6 4.8 3.8 AF181286 unknown 0.05 0.22 8.8 2.7 12.0 35.6 5.9 2.3 AJ272208 IL-1R accessory protein-like 2 0.22 0.17 8.8 2.9 5.0 3.2 9.8 7.3 AF030555 fatty-acid-Coenzyme A ligase 0.10 0.39 8.7 2.2 11.3 9.9 3.0 2.1 AL050125 unknown 0.23 0.07 8.6 14.3 5.2 2.8 18.7 8.3 AB011096 KIAA0524 protein 0.21 0.08 8.5 24.4 4.7 6.8 10.4 7.5 J03068 N-acylaminoacyl-peptide hydrolase 0.54 0.21 8.3 2.4 2.2 4.1 3.0 6.0 M33906 MHC class II, DQ alpha 1 0.14 0.08 7.6 4.5 15.2 6.1 7.5 7.9 AJ272265 secreted phosphoprotein 0.21 0.09 7.6 9.0 3.3 4.9 18.8 14.5 J00210 interferon alpha 13 0.41 0.07 7.2 15.0 2.8 3.1 11.0 4.3 AK001952 hypothetical protein 0.42 0.21 6.9 4.9 2.5 3.1 7.6 4.5 X54131 protein tyrosine phosphatase, 0.09 0.20 6.4 6.5 7.7 15.0 5.6 4.1 receptor type, AF064493 LIM binding domain 2 0.46 0.14 5.9 5.6 2.2 2.9 8.5 5.8 AL117567 DKFZP566O084 protein 0.44 0.22 5.8 3.3 2.9 2.3 5.7 14.9 L40933 phosphoglucomutase 5 0.16 0.03 5.6 11.0 4.8 3.5 8.5 76.3 M27190 regenerating islet-derived 1 alpha 0.19 0.28 5.3 3.0 3.8 3.6 5.8 3.6 AL031121 unknown 0.24 0.09 5.3 3.8 3.2 3.9 3.0 27.9 U27655 regulator of G-protein signalling 0.24 0.29 5.0 9.0 4.5 8.3 4.2 4.5 AB037786 unknown 0.12 0.03 4.7 54.1 2.8 2.3 2.2 11.0 X73113 myosin-binding protein C 0.29 0.13 4.7 6.5 6.0 2.4 6.7 6.3 AB010962 matrix metalloproteinase 0.08 0.12 4.7 6.2 2.4 4.7 10.9 4.2 AL096729 unknown 0.36 0.13 4.7 7.7 3.2 2.4 6.3 6.2 AB018320 Arg/Abl-interacting protein 0.16 0.18 4.6 7.1 3.0 3.3 5.8 8.9 AK001024 guanine nucleotide-binding protein 0.16 0.11 4.6 2.0 9.8 2.6 7.6 14.1 AJ275355 unknown 0.15 0.08 4.6 17.3 5.4 9.2 5.1 5.5 U21931 fructose-bisphosphatase 1 0.48 0.14 4.6 4.3 2.6 2.1 8.4 9.6 X66403 cholinergic receptor 0.17 0.19 4.4 9.0 10.9 9.3 5.1 6.7 X67734 contactin 2 0.25 0.09 4.3 6.8 3.1 5.8 7.9 8.4 U92981 unknown 0.20 0.23 4.3 3.2 4.8 5.6 5.4 6.3 X68879 empty spiracles homolog 1 0.05 0.08 4.3 2.0 12.3 2.7 5.6 4.7 AL137362 unknown 0.22 0.22 4.2 4.1 2.7 4.1 9.3 4.2 NM_001756 corticosteroid binding globulin 0.28 0.13 4.1 10.6 3.9 2.7 10.3 5.5 U80770 unknown 0.31 0.14 4.1 4.1 23.3 2.7 7.0 10.1 AL109792 unknown 0.16 0.19 4.0 4.5 4.3 8.8 8.7 3.9 X65962 cytochrome P-450 0.33 0.05 3.8 25.3 5.7 5.1 19.8 12.0 AK001856 unknown 0.40 0.21 3.8 7.0 2.6 3.1 2.9 7.8 AL022723 MHC, class I, F 0.55 0.18 3.7 5.7 4.4 2.3 3.3 5.2 D38449 putative G protein coupled receptor 0.18 0.09 3.5 11.1 13.3 5.8 4.8 5.2 AL137489 unknown 0.74 0.26 3.3 2.9 2.6 3.3 2.5 5.4 AB000887 small inducible cytokine subfamily A 0.76 0.18 3.3 5.0 2.6 2.4 5.9 10.3 NM_012450 sulfate transporter 1 0.15 0.10 3.3 9.0 10.0 10.9 4.6 8.7 U86529 glutathione S-transferase zeta 1 0.55 0.15 3.2 6.8 4.4 2.3 9.3 5.1 AK001244 unknown 0.79 0.31 3.2 5.5 2.3 2.3 3.9 2.8 AL133602 unknown 0.16 0.21 3.1 7.8 8.7 2.6 4.1 5.6 AB033080 cell cycle progression 8 protein 0.31 0.31 3.1 4.6 3.0 3.5 2.2 4.2 AF023466 putative glycine-N-acyltransferase 0.27 0.18 3.1 5.0 4.2 7.4 10.1 3.8 AL117457 cofilin 2 0.68 0.53 3.0 4.6 3.3 2.4 7.4 3.4 AC007059 unknown 0.37 0.35 3.0 5.7 3.1 2.4 2.6 2.4 U60179 growth hormone receptor 0.34 0.21 2.9 3.5 2.3 3.1 8.0 4.7 M37238 phospholipase C, gamma 2 0.60 0.36 2.9 2.0 3.2 2.1 2.9 4.6 L22569 cathepsin B 0.32 0.12 2.9 2.1 6.2 3.0 13.1 16.7 M80359 MAP/microtubule affinity-regulating 0.37 0.76 2.9 3.1 6.1 7.6 2.1 3.3 kinase 3 S70348 Integrin beta 3 0.58 0.31 2.6 4.8 4.1 2.6 2.6 2.6 L13720 growth arrest-specific 6 0.36 0.26 2.4 2.5 6.8 4.8 3.9 3.7 AL049423 unknown 0.33 0.30 2.4 3.7 3.8 2.8 2.9 3.4 AL050201 unknown 0.68 0.29 2.2 3.1 3.7. 3.0 3.0 2.2 AF050078 growth arrest specific 11 0.87 0.33 2.1 8.4 2.5 2.2 2.6 4.4 AK001753 hypothetical protein 0.53 0.28 2.1 5.0 2.2 2.8 3.6 4.6 X05323 unknown 0.39 0.13 2.1 7.8 2.6 2.4 21.5 3.5 AB014548 KIAA0648 protein 0.61 0.30 2.0 2.4 4.8 3.4 4.9 3.9

TABLE 34 Up-regulation of Polynucleotide expression in A549 cells induced by Formula D Peptides. The peptides at a concentration of 50 μg/ml were shown to increase the expression of many polynucleotides. Peptide was incubated with the human A549 epithelial cells for 4 h and the RNA was isolated, converted into labeled cDNA probes and hybridized to Human Operon arrays (PRHU04). The intensity of polynucleotides in control, unstimulated cells are shown in the second and third columns for labeling of cDNA with the dyes Cy3 and Cy5 respectively. The “ID#: Control” columns refer to the intensity of polynucleotide expression in peptide-simulated cells divided by the intensity of unstimulated cells. Accession control- control- ID 26: ID 27: ID 28: ID 29: ID 30: ID 31: Number Gene Cy3 Cy5 control control control control control control U68018 MAD homolog 2 0.13 0.71 11.2 2.2 8.0 2.3 6.7 25.6 NM_016015 CGI-68 protein 0.92 1.59 2.3 2.3 3.5 3.7 3.4 22.9 AF071510 lecithin retinol acyltransferase 0.07 0.05 15.4 10.3 5.3 44.1 2.1 21.2 AC005154 unkown 0.17 1.13 2.7 7.2 12.6 6.4 3.3 20.6 M81933 cell division cycle 25A 0.13 0.21 4.3 3.1 3.2 4.3 5.6 18.2 AF124735 LIM HOX gene 2 0.17 0.21 2.1 4.4 5.9 5.2 7.6 17.0 AL110125 unknown 0.30 0.08 5.0 2.7 6.8 10.2 2.8 12.0 NM_004732 potassium voltage-gated channel 0.15 0.16 7.6 4.0 3.4 2.2 2.9 11.4 AF030555 fatty-acid-Coenzyme A 0.10 0.39 10.5 2.2 6.4 3.0 5.1 10.7 ligase_long-chain 4 AF000237 1-acylglycerol-3-phosphate 1.80 2.37 3.4 2.5 2.4 2.1 3.7 9.9 O-acyltransferase 2 AL031588 hypothetical protein 0.40 0.26 5.8 20.2 2.8 4.7 5.6 9.1 AL080077 unknown 0.15 0.21 2.4 2.0 11.9 3.8 2.3 8.7 NM_014366 putative nucleotide binding 0.90 2.52 2.4 4.3 2.4 2.6 3.0 8.6 protein_estradiol-induced AB002359 phosphoribosylformylglycinamidine 0.81 2.12 3.2 2.7 5.5 2.5 2.8 6.9 synthase U33547 MHC class II antigen HLA-DRB6 mRNA_(—) 0.14 0.16 2.5 5.3 4.5 5.0 3.1 6.6 AL133051 unknown 0.09 0.07 7.7 6.3 5.4 23.1 5.4 6.5 AK000576 hypothetical protein 0.27 0.06 7.1 9.3 5.0 6.9 2.9 6.2 AF042378 spindle pole body protein 0.36 0.39 3.3 3.0 9.5 4.5 3.4 6.2 AF093265 Homer neuronal immediate early 0.67 0.53 2.7 13.3 6.5 5.0 2.9 6.2 gene_3 D80000 Segregation of mitotic chromosomes 1.01 1.56 3.6 2.5 4.9 3.2 6.3 6.1 1 AF035309 proteasome 26S subunit ATPase 5 3.61 4.71 2.7 6.6 5.2 4.9 2.7 6.0 adaptor-related protein complex 2 M34175 beta 1 subunit 4.57 5.13 3.2 3.1 4.0 4.6 2.7 6.0 AB020659 KIAA0852 protein 0.18 0.37 4.1 7.6 5.7 4.8 2.5 5.7 NM_004862 LPS-induced TNF-alpha factor 2.61 3.36 3.8 4.8 4.1 4.9 3.2 5.6 U00115 zinc finger protein 51 0.51 0.07 18.9 2.2 3.5 7.2 21.2 5.6 AF088868 fibrousheathin II 0.45 0.20 4.7 10.0 3.2 6.4 6.0 5.6 AK001890 unknown 0.42 0.55 2.4 3.5 3.6 2.3 2.2 5.6 AL137268 KIAA0759 protein 0.49 0.34 3.8 2.3 5.0 3.5 3.3 5.4 X63563 polymerase II polypeptide B 1.25 1.68 2.5 8.1 3.4 4.8 5.2 5.4 D12676 CD36 antigen 0.35 0.39 2.9 3.4 2.6 2.2 3.5 5.3 AK000161 hypothetical protein 1.06 0.55 3.4 8.7 2.1 6.7 2.9 5.1 AF052138 unknown 0.64 0.51 2.9 2.8 2.7 5.2 3.6 5.0 AL096803 unknown 0.36 0.03 20.1 18.3 3.7 19.3 16.1 4.9 S49953 DNA-binding transcriptional activator 0.70 0.15 3.7 4.0 2.1 6.6 4.0 4.8 X89399 RAS p21 protein activator 0.25 0.10 8.5 14.9 4.8 18.6 4.3 4.8 AJ005273 antigenic determinant of recA protein 0.70 0.10 7.6 11.1 2.8 9.9 12.0 4.6 AK001154 hypothetical protein 1.70 0.96 2.4 4.4 2.9 8.9 2.4 4.5 AL133605 unknown 0.26 0.15 12.4 4.2 4.4 3.3 3.3 4.1 U71092 G protein-coupled receptor 24 0.53 0.06 19.0 9.1 2.2 12.0 3.3 4.1 AF074723 RNA polymerase II transcriptional 0.67 0.54 4.0 3.2 3.1 3.4 6.0 4.0 regulation mediator AL137577 unknown 0.32 0.12 31.4 6.2 5.3 10.1 25.3 3.9 AF151043 hypothetical protein 0.48 0.35 2.6 2.2 2.0 3.3 2.2 3.8 AF131831 unknown 0.67 0.81 2.1 7.0 3.5 3.2 3.9 3.7 D50405 histone deacetylase 1 1.52 2.62 3.1 7.2 2.9 4.1 2.8 3.7 U78305 protein phosphatase 1D 1.21 0.20 4.7 13.0 3.5 5.9 4.2 3.7 AL035562 paired box gene 1 0.24 0.01 30.2 81.9 5.6 82.3 6.2 3.7 U67156 mitogen-activated protein kinase 1.15 0.30 6.6 3.0 2.2 2.3 2.5 3.6 kinase kinase 5 AL031121 unknown 0.24 0.09 5.2 3.7 2.3 6.5 9.1 3.6 U13666 G protein-coupled receptor 1 0.34 0.14 3.8 5.4 3.1 3.3 2.8 3.6 AB018285 KIAA0742 protein 0.53 0.13 14.9 13.9 5.9 18.5 15.2 3.5 D42053 site-1 protease 0.63 0.40 2.6 7.1 5.6 9.2 2.6 3.5 AK001135 Sec23-interacting protein p125 0.29 0.53 5.7 4.5 3.4 2.6 11.3 3.4 AL137461 unknown 0.25 0.02 23.8 9.0 2.7 59.2 12.5 3.3 NM_006963 zinc finger protein 22 0.10 0.08 3.2 7.6 3.7 7.9 11.2 3.2 AL137540 unknown 0.67 0.79 3.9 2.6 5.6 4.2 3.5 3.1 AL137718 unknown 0.95 0.18 4.7 8.0 4.0 13.3 3.0 3.1 AF012086 RAN binding protein 2-like 1 1.20 0.59 4.6 4.0 2.0 4.6 3.6 3.1 S57296 HER2/neureceptor 0.59 0.17 7.3 12.1 2.3 20.0 22.2 3.0 NM_013329 GC-rich sequence DNA-binding factor 0.16 0.08 6.9 14.3 9.7 3.3 7.2 3.0 candidate AF038664 UDP-Gal:betaGlcN Ac beta 1_4- 0.15 0.03 13.4 22.2 5.4 15.8 1.7.6 3.0 galactosyltransferase AF080579 Homo sapiens integral membrane protein 0.34 1.03 3.3 3.0 6.7 2.1 2.9 2.9 AK001075 hypothetical protein 0.67 0.10 2.1 2.6 2.6 8.9 2.2 2.9 AB011124 KIAA0552 gene product 0.46 0.04 9.6 72.0 6.0 33.9 13.6 2.9 J03068 N-acylaminoacyl-peptide hydrolase 0.54 0.21 2.2 5.0 2.4 5.2 3.6 2.8 D87120 osteoblast protein 0.87 0.87 2.2 2.0 4.7 2.3 2.0 2.8 AB006537 IL-1R accessory protein 0.17 0.07 2.9 7.0 14.5 5.3 6.6 2.8 L34587 transcription elongation factor B 2.49 1.23 2.2 16.3 5.0 15.8 5.5 2.7 D31891 SET domain_bifurcated_1 1.02 0.29 3.9 6.0 4.3 4.9 6.6 2.7 D00760 proteasome subunit_alpha type_2 4.97 4.94 4.1 2.6 2.0 2.8 2.7 2.7 AC004774 distal-less homeo box 5 0.25 0.12 2.3 6.3 3.8 5.2 5.2 2.6 AL024493 unknown 1.46 0.54 4.8 13.5 2.1 11.6 6.8 2.6 AB014536 copine III 1.80 1.29 3.2 9.5 3.8 6.8 2.6 2.6 X59770 IL-1R type II 0.59 0.16 9.6 4.7 3.9 3.2 4.9 2.5 AF052183 unknown 0.65 0.76 4.0 3.7 2.3 5.0 3.0 2.5 AK000541 hypothetical protein 0.92 0.27 4.5 13.9 3.6 18.1 4.3 2.5 U88528 cAMP responsive element binding 1.37 0.86 3.1 5.4 2.1 2.8 2.1 2.4 protein M97925 defensin alpha 5_Paneth cell-specific 0.33 0.07 4.6 35.9 2.0 7.8 6.5 2.4 NM_013393 cell division protein FtsJ 1.38 0.94 3.1 5.8 2.1 4.2 2.6 2.3 X62744 MHC class II DM alpha 0.86 0.32 4.0 4.7 2.3 2.9 6.1 2.3 AF251040 putative nuclear protein 0.64 0.30 6.7 3.4 2.9 3.9 5.7 2.2 AK000227 hypothetical protein 1.49 0.43 3.4 7.1 2.3 3.3 9.1 2.1 U88666 SFRS protein kinase 2 1.78 0.37 3.4 5.9 2.6 8.4 6.1 2.0

TABLE 35 Up-regulation of Polynucleotide expression in A549 cells induced by Formula E Peptides. The peptides at a concentration of 50 μg/ml were shown to increase the expression of many polynucleotides. Peptide was incubated with the human A549 epithelial cells for 4 h and the RNA was isolated, converted into labeled cDNA probes and hybridized to Human Operon arrays (PRHU04). The intensity of polynucleotides in control, unstimulated cells are shown in the second and third columns for labeling of cDNA with the dyes Cy3 and Cy5 respectively. The “ID#: Control” columns refer to the intensity of polynucleotide expression in peptide-simulated cells divided by the intensity of unstimulated cells. Accession control- control- ID 33: ID 34: ID 35: ID 36: ID 37: ID 38: Number Gene Cy3 Cy5 control control control control control control AL049689 Novel human mRNA 0.25 0.05 2.7 26.5 3.3 21.7 5.4 37.9 AK000576 hypothetical protein 0.27 0.06 3.0 19.1 3.9 23.0 3.1 28.3 X74837 mannosidase, alpha class 1A member 1 0.10 0.07 5.6 10.0 10.8 12.3 12.0 19.9 AK000258 hypothetical protein 0.27 0.07 14.0 11.1 7.9 16.1 6.2 18.9 X89067 transient receptor 0.20 0.14 3.7 2.2 2.4 2.6 8.0 18.1 AL137619 unknown 0.16 0.08 6.3 6.7 10.8 10.5 7.9 16.5 NM_003445 zinc finger protein 0.17 0.07 4.0 23.6 2.9 13.6 4.3 14.4 X03084 complement component 1 0.36 0.15 2.4 3.1 2.9 7.7 3.4 13.7 U27330 fucosyltransferase 5 0.39 0.08 2.4 2.5 2.6 12.1 3.5 13.0 AF070549 unknown 0.16 0.09 2.7 4.7 7.9 10.3 4.2 12.6 AB020335 sel-1 -like 0.19 0.24 2.9 2.6 2.0 7.3 4.7 12.4 M26901 renin 0.09 0.12 14.9 2.2 7.3 12.0 20.8 12.0 Y07828 ring finger protein 0.09 0.06 9.0 26.6 8.9 16.0 3.6 11.6 AK001848 hypothetical protein 0.21 0.07 6.2 8.2 2.7 5.2 5.5 10.9 NM_016331 zinc finger protein 0.16 0.08 7.6 5.1 7.0 25.5 5.5 10.9 U75330 neural cell adhesion molecule 2 0.42 0.08 2.5 3.6 2.0 5.8 6.2 9.9 AB037826 unknown 0.16 0.11 3.8 6.0 3.4 13.4 6.0 9.8 M34041 adrenergic alpha-2B-receptor 0.30 0.13 4.5 4.5 3.7 8.6 5.6 9.8 D38449 putative G protein coupled receptor 0.18 0.09 2.3 25.8 11.7 2.3 3.2 9.5 AJ250562 transmembrane 4 superfamily member 2 0.13 0.10 10.0 8.4 2.2 8.1 16.3 9.1 AK001807 hypothetical protein 0.18 0.12 4.2 5.3 4.6 3.2 4.0 8.3 AL133051 unknown 0.09 0.07 5.1 13.6 6.0 9.1 2.2 8.2 U43843 Neuro-d4 homolog 0.61 0.10 2.0 6.4 2.3 16.6 2.2 8.1 NM_013227 aggrecan 1 0.28 0.15 7.5 3.1 2.5 6.9 8.5 7.8 AF226728 somatostatin receptor-interacting 0.23 0.17 7.0 3.6 3.1 5.5 3.5 7.7 protein AK001024 guanine nucleotide-binding protein 0.16 0.11 3.9 12.3 2.7 7.4 3.3 7.0 AC002302 unknown 0.13 0.14 16.1 5.8 5.8 2.6 9.6 6.2 AB007958 unknown 0.17 0.27 2.0 2.3 11.3 3.3 3.0 6.1 AF059293 cytokine receptor-like factor 1 0.19 0.22 3.6 2.5 10.2 3.8 2.7 5.9 V01512 v-fos 0.27 0.21 6.7 3.7 13.7 9.3 3.7 5.4 U82762 sialyltransferase 8 0.23 0.15 3.2 6.5 2.7 9.2 5.7 5.4 U44059 thyrotrophic embryonic factor 0.05 0.13 22.9 7.1 12.5 7.4 9.7 5.4 X05323 antigen identified by monoclonal 0.39 0.13 4.3 2.5 2.2 7.4 2.8 5.1 antibody U72671 ICAM 5, 0.25 0.14 5.3 2.7 3.7 10.0 3.2 4.8 AL133626 hypothetical protein 0.26 0.25 2.2 4.2 2.9 3.0 2.6 4.7 X96401 MAX binding protein 0.31 0.29 6.9 2.3 4.9 3.1 2.9 4.6 AL117533 unknown 0.05 0.26 8.2 2.7 11.1 2.5 11.9 4.5 AK001550 hypothetical protein 0.10 0.30 8.0 2.0 4.9 2.1 7.8 4.5 AB032436 Homo sapiens BNPI mRNA 0.14 0.21 5.1 2.2 9.1 4.5 6.4 4.4 AL035447 hypothetical protein 0.28 0.23 4.3 3.7 8.7 5.2 3.7 4.2 U09414 zinc finger protein 0.28 0.25 4.0 2.2 4.7 3.3 7.2 4.2 AK001256 unknown 0.09 0.08 5.3 6.5 31.1 12.7 6.4 4.1 L14813 carboxyl ester lipase-like 0.64 0.21 2.7 6.2 3.1 2.1 3.4 3.9 AF038181 unknowan 0.06 0.18 34.1 6.4 4.5 8.7 11.3 3.9 NM_001486 glucokinase 0.21 0.08 3.0 2.2 6.5 12.4 5.7 3.9 AB033000 hypothetical protein 0.24 0.22 3.4 3.3 7.1 5.5 4.5 3.8 AL117567 DKFZP566O084 protein 0.44 0.22 2.2 2.7 3.9 4.0 4.5 3.7 NM_012126 carbohydrate sulfotransferase 5 0.31 0.20 5.5 5.4 3.8 5.5 2.6 3.5 AL031687 unknown 0.16 0.27 5.9 2.6 3.4 2.3 4.9 3.5 X04506 apolipoprotein B 0.29 0.32 5.4 4.4 6.9 5.5 2.1 3.5 NM_006641 CCR 9 0.35 0.11 3.3 3.3 2.2 16.5 2.3 3.5 Y00970 acrosin 0.12 0.14 8.2 8.8 3.1 6.2 17.5 3.4 X67098 rTS beta protein 0.19 0.26 2.4 3.1 7.8 3.5 4.4 3.3 U51990 pre-mRNA splicing factor 0.56 0.19 2.2 3.0 2.8 13.7 2.9 3.0 AF030555 fatty-acid-Coenzyme A 0.10 0.39 3.5 6.9 13.3 4.4 7.5 2.9 AL009183 TNFR superfamily, member 9 0.46 0.19 6.0 4.1 2.8 8.6 2.6 2.8 AF045941 sciellin 0.16 0.21 11.6 2.4 2.8 2.2 4.1 2.8 AF072756 A kinase anchor protein 4 0.33 0.07 2.5 5.3 3.9 32.7 2.3 2.7 X78678 ketohexokinase 0.10 0.20 18.0 3.5 4.1 2.5 14.6 2.6 AL031734 unknown 0.03 0.39 43.7 2.3 41.7 4.0 10.8 2.5 D87717 KIAA0013 gene product 0.35 0.42 4.2 2.3 3.6 2.6 2.9 2.5 U01824 solute carrier family 1 0.42 0.29 4.8 2.3 4.2 7.1 4.2 2.4 AF055899 solute carrier family 27 0.14 0.31 9.5 12.3 7.4 4.7 6.6 2.3 U22526 lanosterol synthase 0.09 0.45 4.1 3.4 10.4 2.2 17.9 2.3 AB032963 unknown 0.19 0.34 6.3 6.1 2.9 2.1 5.7 2.2 NM_015974 lambda-crystallin 0.17 0.25 11.4 2.8 5.9 2.4 5.8 2.2 X82200 stimulated trans-acting factor 0.23 0.15 8.2 3.4 3.0 2.8 11.3 2.2 AL137522 unknown 0.12 0.26 12.1 3.7 12.6 6.9 4.3 2.2 Z99916 crystallin, beta B3 0.28 0.65 2.5 2.1 3.6 2.2 2.6 2.1 AF233442 ubiquitin specific protease 21 0.41 0.31 2.6 3.6 3.6 4.5 3.4 2.1 AK001927 hypothetical protein 0.24 0.52 7.6 5.6 5.0 2.5 4.1 2.0

TABLE 36 Up-regulation of Polynucleotide expression in A549 cells induced by Formula F Peptides. The peptides at a concentration of 50 μg/ml were shown to increase the expression of many polynucleotides. Peptide was incubated with the human A549 epithelial cells for 4 h and the RNA was isolated, converted into labeled cDNA probes and hybridized to Human Operon arrays (PRHU04). The intensity of polynucleotides in control, unstimulated cells are shown in the second and third columns for labeling of cDNA with the dyes Cy3 and Cy5 respectively. The “Ratio ID#: Control” columns refer to the intensity of polynucleotide expression in peptide-simulated cells divided by the intensity of unstimulated cells. Ratio Ratio Ratio Ratio Ratio Accession control- control- ID 40: ID 42: ID 43: ID 44: ID 45: Number Gene Cy3 Cy5 control control control control control AF025840 polymerase epsilon 2 0.34 0.96 3.4 2.0 2.0 2.1 4.3 AF132495 CGI-133 protein 0.83 0.67 3.0 2.2 2.6 2.8 5.1 AL137682 hypothetical protein 0.73 0.40 2.0 5.3 4.8 2.9 8.2 U70426 regulator of G-protein signalling 16 0.23 0.25 3.1 3.0 5.3 3.1 12.2 AK001135 Sec23-interacting protein p125 0.29 0.53 3.2 2.6 3.3 14.4 5.2 AB023155 KIAA0938 protein 0.47 0.21 2.7 4.8 8.1 4.2 10.4 AB033080 cell cycle progression 8 protein 0.31 0.31 4.4 2.2 5.9 4.3 6.9 AF061836 Ras association domain family 1 0.29 0.31 3.2 2.5 11.1 18.8 6.8 AK000298 hypothetical protein 0.48 0.27 3.3 2.2 7.1 5.6 7.7 L75847 zinc finger protein 0.35 0.52 3.2 3.0 4.0 3.0 3.9 X97267 protein tyrosine phosphatase 0.19 0.24 4.1 9.3 2.4 4.2 8.3 Z11933 POU domain class 3 TF 2 0.09 0.23 8.7 2.5 3.6 4.3 8.2 AB037744 unknown 0.37 0.57 2.6 2.9 2.7 3.0 3.1 U90908 unknown 0.12 0.16 11.8 7.7 3.4 7.8 11.2 AL050139 unknown 0.29 0.60 5.2 2.4 3.3 3.0 2.8 AB014615 fibroblast growth factor 8 0.19 0.07 5.4 3.5 8.5 3.2 22.7 M28825 CD1A antigen 0.51 0.36 4.1 2.6 2.0 4.6 4.4 U27330 fucosyltransferase 5 0.39 0.08 3.3 2.1 24.5 8.2 19.3 NM_006963 zinc finger protein 0.10 0.08 10.4 12.6 12.3 29.2 20.5 AF093670 peroxisomal biogenesis factor 0.44 0.53 4.0 2.6 2.6 4.3 2.9 AK000191 hypothetical protein 0.50 0.18 2.3 3.6 4.4 2.2 8.2 AB022847 unknown 0.39 0.24 2.1 6.9 4.5 2.8 6.2 AK000358 microfibrillar-associated protein 3 0.28 0.28 5.7 2.0 3.5 5.2 5.2 X74837 mannosidase_alpha class 1A 0.10 0.07 13.1 18.4 23.6 16.3 20.8 AF053712 TNF superfamily_member 11 0.17 0.08 11.3 9.3 13.4 10.6 16.6 AL133114 DKFZP586P2421 protein 0.11 0.32 8.5 3.4 4.9 5.3 4.3 AF049703 E74-like factor 5 0.22 0.24 5.1 6.0 3.3 2.7 5.4 AL137471 hypothetical protein 0.29 0.05 4.0 15.0 10.1 2.7 25.3 AL035397 unknown 0.33 0.14 2.3 2.8 10.6 4.6 9.3 AL035447 hypothetical protein 0.28 0.23 3.8 6.8 2.7 3.0 5.7 X55740 CD73 0.41 0.61 2.1 3.3 2.9 3.2 2.1 NM_004909 taxol resistance associated gene 3 0.20 0.22 3.9 2.9 6.5 3.2 5.6 AF233442 ubiquitin specific protease 0.41 0.31 2.9 4.7 2.7 3.5 3.9 U92980 unknown 0.83 0.38 4.2 4.1 4.8 2.3 3.1 AF105424 myosin heavy polypeptide-like 0.30 0.22 2.8 3.3 4.4 2.3 5.3 M26665 histatin 3 0.29 0.26 7.9 3.5 4.6 3.5 4.5 AF083898 neuro-oncological ventral antigen 2 0.20 0.34 18.7 3.8 2.2 3.6 3.5 AJ009771 ariadne_Drosophila_homolog of 0.33 0.06 2.3 17.6 15.9 2.5 20.3 AL022393 hypothetical protein P1 0.05 0.33 32.9 2.4 3.0 69.4 3.4 AF039400 chloride channel_calcium activated_(—) 0.11 0.19 8.4 2.9 5.1 18.1 5.9 family member 1 AJ012008 dimethylarginine dimethylaminohydrolase 2 0.42 0.43 5.1 3.3 3.2 6.2 2.6 AK000542 hypothetical protein 0.61 0.24 2.1 4.5 5.0 3.7 4.4 AL133654 unknown 0.27 0.40 2.8 2.1 2.5 2.5 2.6 AL137513 unknown 0.43 0.43 6.4 3.2 3.8 2.3 2.3 U05227 GTP-binding protein 0.38 0.36 5.0 3.1 3.1 2.2 2.8 D38449 putative G protein coupled receptor 0.18 0.09 5.8 6.7 6.7 9.1 10.4 U80770 unknown 0.31 0.14 3.9 3.8 6.6 3.1 6.8 X61177 IL-5R alpha 0.40 0.27 2.6 4.4 9.8 8.1 3.6 U35246 vacuolar protein sorting 45A 0.15 0.42 5.8 2.8 2.6 4.5 2.2 AB017016 brain-specific protein p25 alpha 0.27 0.29 6.0 2.6 3.4 3.1 3.1 X82153 cathepsin K 0.45 0.20 4.2 5.2 4.8 4.4 4.6 AC005162 probable carboxypeptidase precursor 0.12 0.28 11.9 3.4 6.8 18.7 3.2 AL137502 unknown 0.22 0.16 3.9 4.9 7.3 3.9 5.3 U66669 3-hydroxyisobutyryl-Coenzyme A hydrolase 0.30 0.40 10.3 3.5 5.2 2.3 2.1 AK000102 unknown 0.39 0.30 2.8 5.3 5.2 4.1 2.8 AF034970 docking protein 2 0.28 0.05 3.3 8.5 15.7 4.0 17.3 AK000534 hypothetical protein 0.13 0.29 6.8 2.3 4.0 20.6 2.9 J04599 biglycan 0.39 0.30 4.0 3.7 4.0 4.8 2.8 AL133612 unknown 0.62 0.33 2.7 3.4 5.2 3.0 2.5 D10495 protein kinase C delta 0.18 0.10 12.0 20.7 8.7 6.8 8.1 X58467 cytochrome P450 0.07 0.24 15.4 4.7 7.9 34.4 3.4 AF131806 unknown 0.31 0.25 2.6 3.4 5.7 7.0 3.2 AK000351 hypothetical protein 0.34 0.13 4.0 6.9 5.5 2.8 6.3 AF075050 hypothetical protein 0.55 0.09 2.7 17.8 5.1 2.2 8.3 AK000566 hypothetical protein unknown 0.15 0.35 6.7 2.2 6.8 6.4 2.1 U43328 cartilage linking protein 1 0.44 0.19 2.5 6.2 6.9 7.8 3.8 AF045941 sciellin 0.16 0.21 6.8 7.5 4.8 6.9 3.4 U27655 regulator of G-protein signalling 3 0.24 0.29 5.5 4.9 2.9 4.9 2.4 AK000058 hypothetical protein 0.25 0.15 5.0 9.7 16.4 2.7 4.5 AL035364 hypothetical protein 0.32 0.26 4.4 4.2 7.3 2.8 2.6 AK001864 unknown 0.40 0.25 3.7 3.7 4.6 3.2 2.6 AB015349 unknown 0.14 0.24 10.5 2.8 3.7 8.0 2.7 V00522 MHC class II DR beta 3 0.62 0.22 4.8 3.9 4.7 2.5 3.0 U75330 neural cell adhesion molecule 2 0.42 0.08 2.1 9.6 13.2 3.3 7.8 NM_007199 IL-1R-associated kinase M 0.15 0.25 8.7 7.8 8.6 16.1 2.5 D30742 calcium/calmodulin-dependent 0.28 0.09 6.2 28.7 7.4 2.4 6.8 protein kinase IV X05978 cystatin A 0.63 0.17 2.7 4.8 9.4 2.2 3.6 AF240467 TLR-7 0.11 0.10 13.8 13.3 4.7 7.7 4.9

TABLE 37 Up-regulation of Polynucleotide expression in A549 cells induced by Formula G and additional Peptides. The peptides at a concentration of 50 μg/ml were shown to increase the expression of many polynucleotides. Peptide was incubated with the human A549 epithelial cells for 4 h and the RNA was isolated, converted into labelled cDNA probes and hybridised to Human Operon arrays (PRHU04). The intensity of polynucleotides in control, unstimulated cells are shown in the second and third columns for labelling of cDNA with the dyes Cy3 and Cy5 respectively. The “Ratio ID#: Control” columns refer to the intensity of polynucleotide expression in peptide-simulated cells divided by the intensity of unstimulated cells. Accession numbers and gene designations are U00115, zinc finger protein; M91036, hemoglobin gamma G; K000070, hypothetical protein; AF055899, solute carrier family 27; AK001490, hypothetical protein; X97674, nuclear receptor coactivator 2; AB022847, unknown; AJ275986, transcription factor; D10495, protein kinase C, delta; L36642, EphA7; M31166, pentaxin-related gene; AF176012, unknown; AF072756, A kinase anchor protein 4; NM_014439, IL-1 Superfamily z; AJ271351, putative transcriptional regulator; AK000576, hypothetical protein; AJ272265, secreted phosphoprotein 2; AL122038, hypothetical protein; AK000307, hypothetical protein; AB029001, KIAA1078 protein; U62437, cholinergic receptor; AF064854, unknown; AL031588, hypothetical protein; X89399, RAS p21 protein activator; D45399, phosphodiesterase; AB037716, hypothetical protein; X79981, cadherin 5; AF034208, RIG-like 7-1; AL133355, chromosome 21 open reading frame 53; NM_016281, STE20-like kinase; AF023614, transmembrane activator and CAML interactor; AF056717, ash2-like; AB029039, KIAA1116 protein; J03634, inhibin, beta A; U80764, unknown; AB032963, unknown; X82835, sodium channel, voltage-gated, type IX Accession control- control- ID 53: ID 54: ID 47: ID 48: ID 49: ID 50: ID 51: ID 52: Number Cy3 Cy5 control control control control control control control control U00115 0.51 0.07 27.4 7.3 2.4 3.1 4.8 8.3 3.5 20.0 M91036 0.22 0.02 39.1 32.5 5.2 2.2 37.0 6.0 16.2 18.0 AK000070 0.36 0.18 3.8 7.6 2.6 15.1 12.2 9.9 17.2 15.3 AF055899 0.14 0.31 6.7 3.7 9.7 10.0 2.2 16.7 5.4 14.8 AK001490 0.05 0.02 14.1 35.8 3.2 28.6 25.0 20.2 56.5 14.1 X97674 0.28 0.28 3.2 3.7 4.0 10.7 3.3 3.1 4.0 13.2 AB022847 0.39 0.24 4.1 4.4 4.5 2.7 3.7 10.4 5.0 11.3 AJ275986 0.26 0.35 5.8 2.3 5.7 2.2 2.5 9.7 4.3 11.1 D10495 0.18 0.10 8.0 3.4 4.6 2.0 6.9 2.5 12.7 10.3 L36642 0.26 0.06 5.8 14.2 2.6 4.1 8.9 3.4 6.5 6.6 M31166 0.31 0.12 4.8 3.8 12.0 3.6 9.8 2.4 8.8 6.4 AF176012 0.45 0.26 3.1 2.9 2.8 2.6 2.3 6.9 3.0 5.8 AF072756 0.33 0.07 9.9 9.3 4.4 4.3 3.2 4.9 11.9 5.4 NM_014439 0.47 0.07 12.0 7.1 3.3 3.3 4.7 5.9 5.0 5.4 AJ271351 0.46 0.12 3.4 3.5 2.3 4.7 2.3 2.7 6.9 5.2 AK000576 0.27 0.06 7.4 15.7 2.9 4.7 9.0 2.4 8.2 5.1 AJ272265 0.21 0.09 6.2 7.9 2.3 3.7 10.3 4.5 4.6 4.7 AL122038 0.46 0.06 6.7 4.5 2.6 4.3 16.4 6.5 26.6 4.6 AK000307 0.23 0.09 3.7 4.0 4.3 3.2 5.3 2.9 13.1 4.4 AB029001 0.52 0.21 14.4 4.3 4.6 4.4 4.8 21.9 3.2 4.2 U62437 0.38 0.13 12.6 6.5 4.2 6.7 2.2 3.7 4.8 3.9 AF064854 0.15 0.16 2.6 2.9 6.2 8.9 14.4 5.0 9.1 3.9 AL031588 0.40 0.26 8.3 5.2 2.8 3.3 5.3 9.0 5.6 3.4 X89399 0.25 0.10 15.8 12.8 7.4 4.2 16.7 6.9 12.7 3.3 D45399 0.21 0.18 3.0 4.7 3.3 4.4 8.7 5.3 5.1 3.3 AB037716 0.36 0.40 5.1 7.5 2.6 2.1 3.5 3.1 2.4 2.8 X79981 0.34 0.10 4.7 7.2 3.2 4.6 6.5 5.1 5.8 2.7 AF034208 0.45 0.24 2.7 10.9 2.1 3.7 2.3 5.9 2.2 2.5 AL133355 0.22 0.23 2.3 3.4 7.3 2.7 3.3 4.3 2.8 2.5 NM_016281 0.40 0.19 6.6 10.6 2.1 2.8 5.0 11.2 10.6 2.5 AF023614 0.11 0.42 2.2 2.2 6.0 7.5 5.0 2.7 2.0 2.4 AF056717 0.43 0.62 4.3 3.2 5.1 4.0 4.6 9.7 3.1 2.2 AB029039 0.79 0.49 2.7 3.3 3.7 2.0 2.3 2.4 4.8 2.2 J03634 0.40 0.12 3.7 2.3 2.3 4.0 10.5 4.1 9.1 2.2 U80764 0.31 0.18 2.3 7.4 4.2 2.3 5.1 3.3 8.8 2.1 AB032963 0.19 0.34 4.0 7.3 5.0 3.0 2.9 6.7 3.8 2.1 X82835 0.25 0.38 2.0 2.7 2.9 7.7 3.3 3.1 3.5 2.0

EXAMPLE 5 Induction of Chemokines in Cell Lines, Whole Human Blood, and in Mice by Peptides

The murine macrophage cell line RAW 264.7, THP-1 cells (human monocytes), a human epithelial cell line (A549), human bronchial epithelial cells (16HBEo14), and whole human blood were used. HBE cells were grown in MEM with Earle's. THP-1 cells were grown and maintained in RPMI 1640 medium. The RAW and A549 cell lines were maintained in DMEM supplemented with 10% fetal calf serum. The cells were seeded in 24 well plates at a density of 10⁶ cells per well in DMEM (see above) and A549 cells were seeded in 24 well plates at a density of 10⁵ cells per well in DMEM (see above) and both were incubated at 37° C. in 5% CO₂ overnight. DMEM was aspirated from cells grown overnight and replaced with fresh medium. After incubation of the cells with peptide, the release of chemokines into the culture supernatant was determined by ELISA (R&D Systems, Minneapolis, Minn.).

Animal studies were approved by the UBC Animal Care Committee (UBC ACC # A01-0008). BALB/c mice were purchased from Charles River Laboratories and housed in standard animal facilities. Age, sex and weight matched adult mice were anaesthetized with an intraperitoneal injection of Avertin (4.4 mM 2-2-2-tribromoethanol, 2.5% 2-methyl-2-butanol, in distilled water), using 200 μl per 10 g body weight. The instillation was performed using a non-surgical, intratracheal instillation method adapted from Ho and Furst 1973. Briefly, the anaesthetized mouse was placed with its upper teeth hooked over a wire at the top of a support frame with its jaw held open and a spring pushing the thorax forward to position the pharynx, larynx and trachea in a vertical straight line. The airway was illuminated externally and an intubation catheter was inserted into the clearly illuminated tracheal lumen. Twenty-μl of peptide suspension or sterile water was placed in a well at the proximal end of the catheter and gently instilled into the trachea with 200 μl of air. The animals were maintained in an upright position for 2 minutes after instillation to allow the fluid to drain into the respiratory tree. After 4 hours the mice were euthanaised by intraperitoneal injection of 300 mg/kg of pentobarbital. The trachea was exposed; an intravenous catheter was passed into the proximal trachea and tied in place with suture thread. Lavage was performed by introducing 0.75 ml sterile PBS into the lungs via the tracheal cannula and then after a few seconds, withdrawing the fluid. This was repeated 3 times with the same sample of PBS. The lavage fluid was placed in a tube on ice and the total recovery volume per mouse was approximately 0.5 ml. The bronchoalveolar lavage (BAL) fluid was centrifuged at 1200 rpm for 10 min, the clear supernatant removed and tested for TNF-α and MCP-1 by ELISA.

The up-regulation of chemokines by cationic peptides was confirmed in several different systems. The murine MCP-1, a homologue of the human MCP-1, is a member of the β(C-C) chemokine family. MCP-1 has been demonstrated to recruit monocytes, NK cells and some T lymphocytes. When RAW 264.7 macrophage cells and whole human blood from 3 donors were stimulated with increasing concentrations of peptide, SEQ ID NO: 1, they produced significant levels of MCP-1 in their supernatant, as judged by ELISA (Table 36). RAW 264.7 cells stimulated with peptide concentrations ranging from 20-50 μg/ml for 24 hr produced significant levels of MCP-1 (200-400 pg/ml above background). When the cells (24 h) and whole blood (4 h) were stimulated with 100 μg/ml of LL-37, high levels of MCP-1 were produced.

The effect of cationic peptides on chemokine induction was also examined in a completely different cell system, A549 human epithelial cells. Interestingly, although these cells produce MCP-1 in response to LPS, and this response could be antagonized by peptide; there was no production of MCP-1 by A549 cells in direct response to peptide, SEQ ID NO: 1. Peptide SEQ ID NO: 1 at high concentrations, did however induce production of IL-8, a neutrophil specific chemokine (Table 37). Thus, SEQ ID NO: 1 can induce a different spectrum of responses from different cell types and at different concentrations. A number of peptides from each of the formula groups were tested for their ability to induce IL-8 in A549 cells (Table 38). Many of these peptides at a low concentration, 10 μg/ml induced IL-8 above background levels. At high concentrations (100 μg/ml) SEQ ID NO: 13 was also found to induce IL-8 in whole human blood (Table 39). Peptide SEQ ID NO: 2 also significantly induced IL-8 in HBE cells (Table 40) and undifferentiated THP-1 cells (Table 41).

BALB/c mice were given SEQ ID NO: 1 or endotoxin-free water by intratracheal instillation and the levels of MCP-1 and TNF-α examined in the bronchioalveolar lavage fluid after 3-4 hr. It was found that the mice treated with 50 μg/ml peptide, SEQ ID NO: 1 produced significantly increased levels of MCP-1 over mice given water or anesthetic alone (Table 42). This was not a pro-inflammatory response to peptide, SEQ ID NO: 1 since peptide did not significantly induce more TNF-α than mice given water or anesthetic alone, peptide, SEQ ID NO: 1 was also found not to significantly induce TNF-α production by RAW 264.7 cells and bone marrow-derived macrophages treated with peptide, SEQ ID NO: 1 (up to 100 μg/ml) (Table 43). Thus, peptide, SEQ ID NO: 1 selectively induces the production of chemokines without inducing the production of inflammatory mediators such as TNF-α. This illustrates the dual role of peptide, SEQ ID NO: 1 as a factor that can block bacterial product-induced inflammation while helping to recruit phagocytes that can clear infections.

TABLE 38 Induction of MCP-1 in RAW 264.7 cells and whole human blood. RAW 264.7 mouse macrophage cells or whole human blood were stimualted with increasing concentrations of LL-37 for 4 hr. The human blood samples were centrifuged and the serum was removed and tested for MCP-1 by ELISA along with the supernatants from the RAW 264.7 cells. The RAW cell data presented is the mean of three or more experiments ± standard error and the human blood data represents the mean ± standard error from three separate donors. Monocyte chemoattractant Peptide, SEQ ID protein (MCP)-1 (pg/ml)* NO: 1 (μg/ml) RAW cells Whole blood 0 135.3 ± 16.3 112.7 ± 43.3 10 165.7 ± 18.2 239.3 ± 113.3 50 367 ± 11.5 371 ± 105 100 571 ± 17.4 596 ± 248.1

TABLE 39 Induction of IL-8 in A549 cells and whole human blood. A549 cells or whole human blood were stimulated with increasing concentrations of peptide for 24 and 4 hr respectively. The human blood samples were centrifuged and the serum was removed and tested for IL-8 by ELISA along with the supernatants from the A549 cells. The A549 cell data presented is the mean of three or more experiments ± standard error and the human blood data represents the mean ± standard error from the three separate donors. Peptide, SEQ ID IL-8 (pg/ml) NO: 1 (μg/ml) A549 cells Whole blood 0 172 ± 29.1 660.7 ± 126.6 1 206.7 ± 46.1 10 283.3 ± 28.4 945.3 ± 279.9 20 392 ± 31.7 50 542.3 ± 66.2 1160.3 ± 192.4 100 1175.3 ± 188.3

TABLE 40 Induction of IL-8 in A549 cells by Cationic peptides. A549 human epithelial cells were stimualted with 10 μg of peptide for 24 hr. The supernatant was removed and tested for IL-8 by ELISA. Peptide (10 ug/ml) IL-8 (ng/ml) No peptide 0.164 LPS, no peptide 0.26 SEQ ID NO: 1 0.278 SEQ ID NO: 6 0.181 SEQ ID NO: 7 0.161 SEQ ID NO: 9 0.21 SEQ ID NO: 10 0.297 SEQ ID NO: 13 0.293 SEQ ID NO: 14 0.148 SEQ ID NO: 16 0.236 SEQ ID NO: 17 0.15 SEQ ID NO: 19 0.161 SEQ ID NO: 20 0.151 SEQ ID NO: 21 0.275 SEQ ID NO: 22 0.314 SEQ ID NO: 23 0.284 SEQ ID NO: 24 0.139 SEQ ID NO: 26 0.201 SEQ ID NO: 27 0.346 SEQ ID NO: 28 0.192 SEQ ID NO: 29 0.188 SEQ ID NO: 30 0.284 SEQ ID NO: 31 0.168 SEQ ID NO: 33 0.328 SEQ ID NO: 34 0.315 SEQ ID NO: 35 0.301 SEQ ID NO: 36 0.166 SEQ ID NO: 37 0.269 SEQ ID NO: 38 0.171 SEQ ID NO: 40 0.478 SEQ ID NO: 41 0.371 SEQ ID NO: 42 0.422 SEQ ID NO: 43 0.552 SEQ ID NO: 44 0.265 SEQ ID NO: 45 0.266 SEQ ID NO: 47 0.383 SEQ ID NO: 48 0.262 SEQ ID NO: 49 0.301 SEQ ID NO: 50 0.141 SEQ ID NO: 51 0.255 SEQ ID NO: 52 0.207 SEQ ID NO: 53 0.377 SEQ ID NO: 54 0.133

TABLE 41 Induction by Peptide of IL-8 in human blood. Whole human blood was stimulated with the increasing concentrations of peptide for 4 hr. The human blood samples were centrifuged and the serum was removed and tested for IL-8 by ELISA. The data shown is the average 2 donors. SEQ ID NO: 3 (μg/ml) IL-8 (pg/ml) 0 85 10 70 100 323

TABLE 42 Induction of IL-8 in HBE cells. Increasing concentrations of the peptide were incubated with HBE cells for 8 h, the supernantant removed and tested for IL-8. The data is presented as the mean of three or more experiments ± standard error. SEQ ID NO: 2 (μg/ml) IL-8 (pg/ml) 0 552 ± 90 0.1 670 ± 155 1 712 ± 205 10 941 ± 15 50 1490 ± 715

TABLE 43 Induction of IL-8 in undifferentiated THP-1 cells. The human monocyte THP-1 cells were incubated with indicated concentrations of peptide for 8 hr. The supernatant was removed and tested for IL-8 by ELISA. SEQ ID NO: 3(μg/ml) IL-8 (pg/ml) 0 10.6 10 17.2 50 123.7

TABLE 44 Induction of MCP-1 by Peptide, SEQ ID NO: 1 in mouse airway. BALB/c mice were anaesthetised with avertin and given intratracheal instillation of peptide or water or no instillation (no treatment). The mice were monitored for 4 hrs, anaesthetised and the BAL fluid was isolated and analyzed for MCP-1 and TNF-α concentrations by ELISA. The data shown is the mean of 4 or 5 mice for each condition ± standard error. Condition MCP-1 (pg/ml) TNF-α (pg/ml) Water 16.5 ± 5 664 ± 107 peptide 111 ± 30 734 ± 210 Avertin 6.5 ± 0.5 393 ± 129

TABLE 45 Lack of Significant TNF-α induction by the Cationic Peptides. RAW 264.7 macrophage cells were incubated with indicated peptides (40 μg/ml) for 6 hours. The supernatant was collected and tested for levels of TNF-α by ELISA. The data is presented as the mean of three or more experiments + standard error. Peptide Treatment TNF-α (pg/ml) Media background 56 ± 8 LPS treatment, No peptide 15207 ± 186 SEQ ID NO: 1 274 ± 15 SEQ ID NO: 5 223 ± 45 SEQ ID NO: 6 297 ± 32 SEQ ID NO: 7 270 ± 42 SEQ ID NO: 8 166 ± 23 SEQ ID NO: 9 171 ± 33 SEQ ID NO: 10 288 ± 30 SEQ ID NO: 12 299 ± 65 SEQ ID NO: 13 216 ± 42 SEQ ID NO: 14 226 ± 41 SEQ ID NO: 15 346 ± 41 SEQ ID NO: 16 341 ± 68 SEQ ID NO: 17 249 ± 49 SEQ ID NO: 19 397 ± 86 SEQ ID NO: 20 285 ± 56 SEQ ID NO: 21 263 ± 8 SEQ ID NO: 22 195 ± 42 SEQ ID NO: 23 254 ± 58 SEQ ID NO: 24 231 ± 32 SEQ ID NO: 26 281 ± 34 SEQ ID NO: 27 203 ± 42 SEQ ID NO: 28 192 ± 26 SEQ ID NO: 29 242 ± 40 SEQ ID NO: 31 307 ± 71 SEQ ID NO: 33 196 ± 42 SEQ ID NO: 34 204 ± 51 SEQ ID NO: 35 274 ± 76 SEQ ID NO: 37 323 ± 41 SEQ ID NO: 38 199 ± 38 SEQ ID NO: 43 947 ± 197 SEQ ID NO: 44 441 ± 145 SEQ ID NO: 45 398 ± 90 SEQ ID NO: 48 253 ± 33 SEQ ID NO: 49 324 ± 38 SEQ ID NO: 50 311 ± 144 SEQ ID NO: 53 263 ± 40 SEQ ID NO: 54 346 ± 86

EXAMPLE 6 Cationic Peptides Increase Surface Expression of Chemokine Receptors

To analyze cell surface expression of IL-8RB, CXCR-4, CCR2, and LFA-1, RAW macrophage cells were stained with 10 μg/ml of the appropriate primary antibody (Santa Cruz Biotechnology) followed by FITC-conjugated goat anti-rabbit IgG [IL-8RB and CXCR-4 (Jackson ImmunoResearch Laboratories, West Grove, Pa.)] or FITC-conjugated donkey anti-goat IgG (Santa Cruz). The cells were analyzed using a FACscan, counting 10,000 events and gating on forward and side scatter to exclude cell debris.

The polynucleotide array data suggested that some peptides up-regulate the expression of the chemokine receptors IL-8RB, CXCR-4 and CCR2 by 10, 4 and 1.4 fold above unstimulated cells respectively. To confirm the polynucleotide array data, the surface expression was examined by flow cytometry of these receptors on RAW cells stimulated with peptide for 4 hr. When 50 μg/ml of peptide was incubated with RAW cells for 4 hr, IL-8RB was up-regulated an average of 2.4-fold above unstimulated cells, CXCR-4 was up-regulated an average of 1.6-fold above unstimulated cells and CCR2 was up-regulated 1.8-fold above unstimulated cells (Table 46). As a control CEMA was demonstrated to cause similar up-regulation. Bac2A was the only peptide to show significant up-regulation of LFA-1 (3.8 fold higher than control cells).

TABLE 46 Increased surface expression of CXCR-4, IL-8RB and CCR2 in response to peptides. RAW macrophage cells were stimulated with peptide for 4 hr. The cells were washed and stained with the appropriate primary and FITC-labeled secondary antibodies. The data shown represents the average (fold change of RAW cells stimulated with peptide from media) ± standard error. Concentration Fold Increase in Protein Expression Peptide (μg/ml) IL-8RB CXCR-4 CCR2 SEQ ID 10 1.0 1.0 1.0 NO: 1 SEQ ID 50 1.3 ± 0.05 1.3 ± 0.03 1.3 + 0.03 NO: 1 SEQ ID 100 2.4 ± 0.6 1.6 ± 0.23 1.8 ± 0.15 NO: 1 SEQ ID 100 2.0 ± 0.6 Not Done 4.5 NO: 3 CEMA 50 1.6 ± 0.1 1.5 ± 0.2 1.5 ± 0.15 100 3.6 ± 0.8 Not Done 4.7 ± 1.1

EXAMPLE 7 Phosphorylation of Map Kinases by Cationic Peptides

The cells were seeded at 2.5×10⁵-5×10⁵ cells/ml and left overnight. They were washed once in media, serum starved in the morning (serum free media—4 hrs). The media was removed and replaced with PBS, then sat at 37° C. for 15 minutes and then brought to room temp for 15 minutes. Peptide was added (concentrations 0.1 ug/ml-50 ug/ml) or H₂O and incubated 10 min. The PBS was very quickly removed and replaced with ice-cold radioimmunoprecipitation (RIPA) buffer with inhibitors (NaF, B-glycerophosphate, MOL, Vanadate, PMSF, Leupeptin Aprotinin). The plates were shaken on ice for 10-15 min or until the cells were lysed and the lysates collected. The procedure for THP-1 cells was slightly different; more cells (2×10⁶) were used. They were serum starved overnight, and to stop the reaction 1 ml of ice-cold PBS was added then they sat on ice 5-10 min, were spun down then resuspended in RIPA. Protein concentrations were determined using a protein assay (Pierce, Rockford, Ill.). Cell lysates (20 μg of protein) were separated by SDS-PAGE and transferred to nitrocellulose filters. The filters were blocked for 1 h with 10 mM Tris-HCl, pH 7.5, 150 mM NaCl (TBS)/5% skim milk powder and then incubated overnight in the cold with primary antibody in TBS/0.05% Tween 20. After washing for 30 min with TBS/0.05% Tween 20, the filters were incubated for 1 h at room temperature with 1 μg/ml secondary antibody in TBS. The filters were washed for 30 min with TBS/0.05% Tween 20 and then incubated 1 h at room temperature with horseradish peroxidase-conjugated sheep anti-mouse IgG (1:10,000 in TBS/0.05% Tween 20). After washing the filters for 30 min with TBS/0.1% Tween 20, immunoreactive bands were visualized by enhanced chemiluminescence (ECL) detection. For experiments with peripheral blood mononuclear cells: The peripheral blood (50-100 ml) was collected from all subjects. Mononuclear cells were isolated from the peripheral blood by density gradient centrifugation on Ficoll-Hypaque. Interphase cells (mononuclear cells) were recovered, washed and then resuspended in recommended primary medium for cell culture (RPMI-1640) with 10% fetal calf serum (FCS) and 1% L-glutamine. Cells were added to 6 well culture plates at 4×10⁶ cells/well and were allowed to adhere at 37° C. in 5% CO₂ atmosphere for 1 hour. The supernatant medium and non-adherent cells were washed off and the appropriate media with peptide was added. The freshly harvested cells were consistently >99% viable as assessed by their ability to exclude trypan blue. After stimulation with peptide, lysates were collected by lysing the cells in RIPA buffer in the presence of various phosphatase- and kinase-inhibitors. Protein content was analyzed and approximately 30 μg of each sample was loaded in a 12% SDS-PAGE gel. The gels were blotted onto nitrocellulose, blocked for 1 hour with 5% skim milk powder in Tris buffered saline (TBS) with 1% Triton X 100. Phosphorylation was detected with phosphorylation-specific antibodies.

The results of peptide-induced phosphorylation are summarized in Table 46. SEQ ID NO: 2 was found to cause dose dependent phosphorylation of p38 and ERK1/2 in the mouse macrophage RAW cell line and the HBE cells. SEQ ID NO: 3 caused phosphorylation of MAP kinases in THP-1 human monocyte cell line and phosphorylation of ERK1/2 in the mouse RAW cell line.

TABLE 47 Phosphorylation of MAP kinases in response to peptides. MAP kinase phosphorylated Cell Line Peptide p38 ERK1/2 RAW 264.7 SEQ ID NO: 3 − + SEQ ID NO: 2 + + HBE SEQ ID NO: 3 + SEQ ID NO: 2 + + THP-1 SEQ ID NO: 3 + + SEQ ID NO: 2

TABLE 48 Peptide Phosphorylation of MAP kinases in human blood monocytes. SEQ ID NO: 1 at 50 μg/ml) was used to promote physphorylation. p38 phosphorylation ERK1/2 phosphorylation 15 minutes 60 minutes 15 minutes 60 minutes + − + +

EXAMPLE 8 Cationic Peptides Protect Against Bacterial Infection by Enhancing the Immune Response

BALB/c mice were given 1×10⁵ Salmonella and cationic peptide (200 μg) by intraperitoneal injection. The mice were monitored for 24 hours at which point they were euthanized, the spleen removed, homogenized and resuspended in PBS and plated on Luria Broth agar plates with Kanamycin (50 μg/ml). The plates were incubated overnight at 37° C. and counted for viable bacteria (Table 49 and 50). CD-1 mice were given 1×10⁸ S. aureus in 5% porcine mucin and cationic peptide (200 μg) by intraperitoneal injection (Table 51). The mice were monitored for 3 days at which point they were euthanized, blood removed and plated for viable counts. CD-1 male mice were given 5.8×10⁶ CFU EHEC bacteria and cationic peptide (200 μg) by intraperitoneal (IP) injection and monitored for 3 days (Table 52). In each of these animal models a subset of the peptides demonstrated protection against infections. The most protective peptides in the Salmonella model demonstrated an ability to induce a common subset of genes in epithelial cells (Table 53) when comparing the protection assay results in Tables 50 and 51 to the gene expression results in Tables 31-37. This clearly indicates that there is a pattern of gene expression that is consistent with the ability of a peptide to demonstrate protection. Many of the cationic peptides were shown not to be directly antimicrobial as tested by the Minimum Inhibitory Concentration (MIC) assay (Table 54). This demonstrates that the ability of peptides to protect against infection relies on the ability of the peptide to stimulate host innate immunity rather than on direct antimicrobial activity.

TABLE 49 Effect of Cationic Peptides on Salmonella Infection in BALB/c mice. The BALB/c mice were injected IP with Salmonella and Peptide, and 24 h later the animals were euthanized, the spleen removed, homogenized, diluted in PBS and plate counts were done to determine bacteria viability. Viable Bacteria Statistical Peptide in the Spleen Significance Treatment (CFU/ml) (p value) Control 2.70 ± 0.84 × 10⁵ SEQ ID NO: 1 1.50 ± 0.26 × 10⁵ 0.12 SEQ ID NO: 6 2.57 ± 0.72 × 10⁴ 0.03 SEQ ID NO: 13 3.80 ± 0.97 × 10⁴ 0.04 SEQ ID NO: 17 4.79 ± 1.27 × 10⁴ 0.04 SEQ ID NO: 27 1.01 ± 0.26 × 10⁵ 0.06

TABLE 50 Effect of Cationic Peptides on Salmonella Infection in BALB/c mice. The BALB/c mice were injected intraperitoneally with Salmonella and Peptide, and 24 h later the animals were euthanized, the spleen removed, homogenized, diluted in PBS and plate counts were done to determine bacteria viability. Peptide Treatment Viable Bacteria in the Spleen (CFU/ml) Control 1.88 ± 0.16 × 10⁴ SEQ ID NO: 48 1.98 ± 0.18 × 10⁴ SEQ ID NO: 26 7.1 ± 1.37 × 10⁴ SEQ ID NO: 30 5.79 ± 0.43 × 10³ SEQ ID NO: 37 1.57 ± 0.44 × 10⁴ SEQ ID NO: 5 2.75 ± 0.59 × 10⁴ SEQ ID NO: 7 5.4 ± 0.28 × 10³ SEQ ID NO: 9 1.23 ± 0.87 × 10⁴ SEQ ID NO: 14 2.11 ± 0.23 × 10³ SEQ ID NO: 20 2.78 ± 0.22 × 10⁴ SEQ ID NO: 23 6.16 ± 0.32 × 10⁴

TABLE 51 Effect of Cationic Peptides in a Murine S. aureus infection model. CD-1 mice were given 1 × 10⁸ bacteria in 5% porcine mucin via intraperitoneal (IP) injection. Cationic peptide (200 μg) was given via a sepearte IP injection. The mice were monitored for 3 days at which point they were euthanized, blood removed and plated for viable counts. The following peptides were not effective in controlling S. aureus infection: SEQ ID NO: 48, SEQ ID NO: 26 # Mice Survived (3 days)/Total Treatment CFU/ml (blood) mice in group No Peptide 7.61 ± 1.7 × 10³ 6/8 SEQ ID NO: 1 0 4/4 SEQ ID NO: 27 2.25 ± 0.1 × 10² 3/4 SEQ ID NO: 30 1.29 ± 0.04 × 10² 4/4 SEQ ID NO: 37 9.65 ± 0.41 × 10² 4/4 SEQ ID NO: 5 3.28 ± 1.7 × 10³ 4/4 SEQ ID NO: 6 1.98 ± 0.05 × 10² 3/4 SEQ ID NO: 7 3.8 ± 0.24 × 10³ 4/4 SEQ ID NO: 9 2.97 ± 0.25 × 10² 4/4 SEQ ID NO: 13 4.83 ± 0.92 × 10³ 3/4 SEQ ID NO: 17 9.6 ± 0.41 × 10² 4/4 SEQ ID NO: 20 3.41 ± 1.6 × 10³ 4/4 SEQ ID NO: 23 4.39 ± 2.0 × 10³ 4/4

TABLE 52 Effect of Peptide in a Murine EHEC infection model. CD-1 male mice (5 weeks old) were given 5.8 × 10⁶ CFU EHEC bacteria via intraperitoneal (IP) injection. Cationic peptide (200 μg) was given via a separate IP injection. The mice were monitored for 3 days. Treatment Peptide Survival (%) control none 25 SEQ ID NO: 23 200 μg 100

TABLE 53 Up-regulation of patterns of gene expression in A549 epithelial cells induced by peptides that are active in vivo. The peptides SEQ ID NO: 30, SEQ ID NO: 7 and SEQ ID NO: 13 at concentrations of 50 μg/ml were each shown to increase the expression of a pattern of genes after 4 h treatment. Peptide was incubated with the human A549 epithelial cells for 4 h and the RNA was isolated, converted into labelled cDNA probes and hybridised to Human Operon arrays (PRHU04). The intensity of polynucleotides in control, unstimulated cells are shown in the second columns for labelling of cDNA (average of Cy3 and Cy5). The Fold Up regulation column refers to the intensity of polynucleotide expression in peptide-simulated cells divided by the intensity of unstimulated cells. The SEQ ID NO: 37 peptide was included as a negative control that was not active in the murine infection models. Fold Up regulation of Gene Expression relative to Untreated Cells Unstimulated SEQ ID SEQ ID SEQ ID SEQ ID Target (Accession number) Cell Intensity NO: 30 NO: 7 NO: 13 NO: 37 Zinc finger protein (AF061261) 13 2.6 9.4 9.4 1.0 Cell cycle gene (S70622) 1.62 8.5 3.2 3.2 0.7 IL-10 Receptor (U00672) 0.2 2.6 9 4.3 0.5 Transferase (AF038664) 0.09 12.3 9.7 9.7 0.1 Homeobox protein (AC004774) 0.38 3.2 2.5 2.5 1.7 Forkhead protein (AF042832) 0.17 14.1 3.5 3.5 0.9 Unknown (AL096803) 0.12 4.8 4.3 4.3 0.6 KIAA0284 Protein (AB006622) 0.47 3.4 2.1 2.1 1.3 Hypothetical Protein (AL022393) 0.12 4.4 4.0 4.0 0.4 Receptor (AF112461) 0.16 2.4 10.0 10.0 1.9 Hypothetical Protein (AK002104) 0.51 4.7 2.6 2.6 1.0 Protein (AL050261) 0.26 3.3 2.8 2.8 1.0 Polypeptide (AF105424) 0.26 2.5 5.3 5.3 1.0 SPR1 protein (AB031480) 0.73 3.0 2.7 2.7 1.3 Dehydrogenase (D17793) 4.38 2.3 2.2 2.2 0.9 Transferase (M63509) 0.55 2.7 2.1 2.1 1.0 Peroxisome factor (AB013818) 0.37 3.4 2.9 2.9 1.4

TABLE 54 Most cationic peptides studied here and especially the cationic peptides effective in infection models are not significantly antimicrobial. A dilution series of peptide was incubated with the indicated bacteria overnight in a 96-well plate. The lowest concentration of peptide that killed the bacteria was used as the MIC. The symbol > indicates the MIC is too large to measure. An MIC of 8 μg/ml or less was considered clinically meaningful activity. Abbreviations: E. coli, Escherichia coli; S. aureus, Staphylococcus aureus; P. aerug, Pseudomonas aeruginosa; S. Typhim, Salmonella enteritidis ssp. typhimurium, C. rhod, Citobacter rhodensis; EHEC, Enterohaemorrhagic E. coli. MIC (μg/ml) Peptide E. coli S. aureus P. aerug. S. typhim. C. rhod. EHEC Polymyxin 0.25 16 0.25 0.5 0.25 0.5 Gentamicin 0.25 0.25 0.25 0.25 0.25 0.5 SEQ ID NO: 1 32 > 96 64 8 4 SEQ ID NO: 5 128 > > > 64 64 SEQ ID NO: 6 128 > > 128 64 64 SEQ ID NO: 7 > > > > > > SEQ ID NO: 8 > > > > > > SEQ ID NO: 9 > > > > > > SEQ ID NO: 10 > > > > > 64 SEQ ID NO: 12 > > > > > > SEQ ID NO: 13 > > > > > > SEQ ID NO: 14 > > > > > > SEQ ID NO: 15 128 > > > 128 64 SEQ ID NO: 16 > > > > > > SEQ ID NO: 17 > > > > > > SEQ ID NO: 19 8 16 16 64 4 4 SEQ ID NO: 2 4 16 32 16 64 SEQ ID NO: 20 8 8 8 8 16 8 SEQ ID NO: 21 64 64 96 64 32 32 SEQ ID NO: 22 8 12 24 8 4 4 SEQ ID NO: 23 4 8 8 16 4 4 SEQ ID NO: 24 16 16 4 16 16 4 SEQ ID NO: 26 0.5 32 64 2 2 0.5 SEQ ID NO: 27 8 64 64 16 2 4 SEQ ID NO: 28 > > > 64 64 128 SEQ ID NO: 29 2 > > 16 32 4 SEQ ID NO: 30 16 > 128 16 16 4 SEQ ID NO: 31 > > 128 > > 64 SEQ ID NO: 33 16 32 > 16 64 8 SEQ ID NO: 34 8 > > 32 64 8 SEQ ID NO: 35 4 128 64 8 8 4 SEQ ID NO: 36 32 > > 32 32 16 SEQ ID NO: 37 > > > > > > SEQ ID NO: 38 0.5 32 64 4 8 4 SEQ ID NO: 40 4 32 8 4 4 2 SEQ ID NO: 41 4 64 8 8 2 2 SEQ ID NO: 42 1.5 64 4 2 2 1 SEQ ID NO: 43 8 128 16 16 8 4 SEQ ID NO: 44 8 > 128 128 64 64 SEQ ID NO: 45 8 > 128 128 16 16 SEQ ID NO: 47 4 > 16 16 4 4 SEQ ID NO: 48 16 > 128 16 1 2 SEQ ID NO: 49 4 > 16 8 4 4 SEQ ID NO: 50 8 > 16 16 16 8 SEQ ID NO: 51 4 > 8 32 4 8 SEQ ID NO: 52 8 > 32 8 2 2 SEQ ID NO: 53 4 > 8 8 16 8 SEQ ID NO: 54 64 > 16 64 16 32

EXAMPLE 9 Use of Polynucleotides Induced by Bacterial Signaling Molecules in Diagnostic/Screening

S. typhimurium LPS and E. coli 0111:B4 LPS were purchased from Sigma Chemical Co. (St. Louis, Mo.). LTA (Sigma) from S. aureus, was resuspended in endotoxin free water (Sigma). The Limulus amoebocyte lysate assay (Sigma) was performed on LTA preparations to confirm that lots were not significantly contaminated by endotoxin (i.e. <1 ng/ml, a concentration that did not cause significant cytokine production in the RAW cell assay). The CpG oligodeoxynucleotides were synthesized with an Applied Biosystems Inc., Model 392 DNA/RNA Synthesizer, Mississauga, ON., then purified and resuspended in endotoxin-free water (Sigma). The following sequences were used CpG: 5′-TCATGACGTTCCTGACGTT-3′ (SEQ ID NO: 57) and nonCpG: 5′-TTCAGGACTTTCCTCAGGTT-3′ (SEQ ID NO: 58). The nonCpG oligo was tested for its ability to stimulate production of cytokines and was found to cause no significant production of TNF-α or IL-6 and therefore was considered as a negative control. RNA was isolated from RAW 264.7 cells that had been incubated for 4 h with medium alone, 100 ng/ml S. typhimurium LPS, 1 μg/ml S. aureus LTA, or 1 μM CpG (concentrations that led to optimal induction of tumor necrosis factor (TNF-α) in RAW cells). The RNA was used to polynucleotiderate cDNA probes that were hybridized to Clontech Atlas polynucleotide array filters, as described above. The hybridization of the cDNA probes to each immobilized DNA was visualized by autoradiography and quantified using a phosphorimager. Results from at least 2 to 3 independent experiments are summarized in Tables 55-59. It was found that LPS treatment of RAW 264.7 cells resulted in increased expression of more than 60 polynucleotides including polynucleotides encoding inflammatory proteins such as IL-1β, inducible nitric oxide synthase (iNOS), MIP-1α, MIP-1β, MIP-2α, CD40, and a variety of transcription factors. When the changes in polynucleotide expression induced by LPS, LTA, and CpG DNA were compared, it was found that all three of these bacterial products increased the expression of pro-inflammatory polynucleotides such as iNOS, MIP-1α, MIP-2α, IL-1β, IL-15, TNFR1 and NF-κB to a similar extent (Table 57). Table 57 describes 19 polynucleotides that were up-regulated by the bacterial products to similar extents in that their stimulation ratios differed by less than 1.5 fold between the three bacterial products. There were also several polynucleotides that were down-regulated by LPS, LTA and CpG to a similar extent. It was also found that there were a number of polynucleotides that were differentially regulated in response to the three bacterial products (Table 58), which includes many of these polynucleotides that differed in expression levels by more than 1.5 fold between one or more bacterial products). LTA treatment differentially influenced expression of the largest subset of polynucleotides compared to LPS or CpG, including hyperstimulation of expression of Jun-D, Jun-B, Elk-1 and cyclins G2 and A1. There were only a few polynucleotides whose expression was altered more by LPS or CpG treatment. Polynucleotides that had preferentially increased expression due to LPS treatment compared to LTA or CpG treatment included the cAMP response element DNA-binding protein 1 (CRE-BPI), interferon inducible protein 1 and CACCC Box-binding protein BKLF. Polynucleotides that had preferentially increased expression after CpG treatment compared to LPS or LTA treatment included leukemia inhibitory factor (LIF) and protease nexin 1 (PN-1). These results indicate that although LPS, LTA, and CpG DNA stimulate largely overlapping polynucleotide expression responses, they also exhibit differential abilities to regulate certain subsets of polynucleotides.

The other polynucleotide arrays used are the Human Operon arrays (identification number for the genome is PRHU04-S1), which consist of about 14,000 human oligos spotted in duplicate. Probes were prepared from 5 μg of total RNA and labeled with Cy3 or Cy5 labeled dUTP. In these experiments, A549 epithelial cells were plated in 100 mm tissue culture dishes at 2.5×10⁶ cells/dish, incubated overnight and then stimulated with 100 ng/ml E. coli O111:B4 LPS for 4 h. Total RNA was isolated using RNAqueous (Ambion). DNA contamination was removed with DNA-free kit (Ambion). The probes prepared from total RNA were purified and hybridized to printed glass slides overnight at 42° C. and washed. After washing, the image was captured using a Perkin Elmer array scanner. The image processing software (Imapolynucleotide 5.0, Marina Del Rey, Calif.) determines the spot mean intensity, median intensities, and background intensities. An “in house” program was used to remove background. The program calculates the bottom 10% intensity for each subgrid and subtracts this for each grid. Analysis was performed with Polynucleotidespring software (Redwood City, Calif.). The intensities for each spot were normalized by taking the median spot intensity value from the population of spot values within a slide and comparing this value to the values of all slides in the experiment. The relative changes seen with cells treated with LPS compared to control cells can be found in the Tables below. A number of previously unreported changes that would be useful in diagnosing infection are described in Table 60.

To confirm and assess the functional significance of these changes, the levels of selected mRNAs and proteins were assessed and quantified by densitometry. Northern blots using a CD 14, vimentin, and tristetraprolin-specific probe confirmed similar expression after stimulation with all 3 bacterial products (Table 60). Similarly measurement of the enzymatic activity of nitric oxide synthetase, iNOS, using Griess reagent to assess levels of the inflammatory mediator NO, demonstrated comparable levels of NO produced after 24 h, consistent with the similar up-regulation of iNOS expression (Table 59). Western blot analysis confirmed the preferential stimulation of leukemia inhibitory factor (LIF, a member of the IL-6 family of cytokines) by CpG (Table 59). Other confirmatory experiments demonstrated that LPS up-regulated the expression of TNF-α and IL-6 as assessed by ELISA, and the up-regulated expression of MIP-2α, and IL-1β mRNA and down-regulation of DP-1 and cyclin D mRNA as assessed by Northern blot analysis. The analysis was expanded to a more clinically relevant ex vivo system, by examining the ability of the bacterial elements to stimulate pro-inflammatory cytokine production in whole human blood. It was found that E. coli LPS, S. typhimurium LPS, and S. aureus LTA all stimulated similar amounts of serum TNF-α, and IL-1β. CpG also stimulated production of these cytokines, albeit to much lower levels, confirming in part the cell line data.

TABLE 55 Polynucleotides Up-regulated by E. coli O111:B4 LPS in A549 Epithelial Cells. E. coli O111:B4 LPS (100 ng/ml) increased the expression of many polynucleotides in A549 cells as studied by polynucleotide microarrays. LPS was incubated with the A549 cells for 4 h and the RNA was isolated. 5 μg total RNA was used to make Cy3/Cy5 labelled cDNA probes and hybridised onto Human Operon arrays (PRHU04). The intensity of unstimulated cells is shown in the second column of Table 55. The “Ratio: LPS/control” column refers to the intensity of polynucleotide expression in LPS simulated cells divided by in the intensity of unstimulated cells. Accession Control: Media Ratio: Number Gene only Intensity LPS/control D87451 ring finger 715.8 183.7 protein 10 AF061261 C3H-type zinc 565.9 36.7 finger protein D17793 aldo-keto reductase 220.1 35.9 family 1, member C3 M14630 prothymosin, alpha 168.2 31.3 AL049975 Unknown 145.6 62.3 L04510 ADP-ribosylation 139.9 213.6 factor domain protein 1, 64kD U10991 G2 protein 101.7 170.3 U39067 eukaryotic trans- 61.0 15.9 lation initiation factor 3, subunit 2 X03342 ribosomal protein 52.6 10.5 L32 NM_004850 Rho-associated, 48.1 11.8 coiled-coil con- taining protein kinase 2 AK000942 Unknown 46.9 8.4 AB040057 serine/threonine 42.1 44.3 protein kinase MASK AB020719 KIAA0912 protein 41.8 9.4 AB007856 FEM-1-like death 41.2 15.7 receptor binding protein J02783 procollagen-proline, 36.1 14.1 2-oxoglutarate 4-dioxygenase AL137376 Unknown 32.5 17.3 AL137730 Unknown 29.4 11.9 D25328 phosphofructo- 27.3 8.5 kinase, platelet AF047470 malate dehydro- 25.2 8.2 genase 2, NAD M86752 stress-induced- 22.9 5.9 phosphoprotein 1 M90696 cathepsin S 19.6 6.8 AK001143 Unknown 19.1 6.4 AF038406 NADH dehydro-genase 17.7 71.5 AK000315 hypothetical protein 17.3 17.4 FLJ20308 M54915 pim-1 oncogene 16.0 11.4 D29011 proteasome subunit, 15.3 41.1 beta type, 5 AK000237 membrane protein 15.1 9.4 of cholinergic synaptic vesicles AL034348 Unknown 15.1 15.8 AL161991 Unknown 14.2 8.1 AL049250 Unknown 12.7 5.6 AL050361 PTD017 protein 12.6 13.0 U74324 RAB interacting 12.3 5.2 factor M22538 NADH dehydrogenase 12.3 7.6 D87076 KIAA0239 protein 11.6 6.5 NM_006327 translocase of inner 11.5 10.0 mitochondrial mem- brane 23 (yeast) homolog AK001083 Unknown 11.1 8.6 AJ001403 mucin 5, subtype B, 10.8 53.4 tracheobronchial M64788 RAP1, GTPase 10.7 7.6 activating protein 1 X06614 retinoic acid re- 10.7 5.5 ceptor, alpha U85611 calcium and integring 10.3 8.1 binding protein U23942 cytochrome P450, 51 10.1 10.2 AL031983 Unknown 9.7 302.8 NM_007171 protein-O-mannosyl- 9.5 6.5 transferase 1 AK000403 hypothetical protein 9.5 66.6 FLJ20396 NM_002950 ribophorin I 9.3 35.7 L05515 cAMP response element- 8.9 6.2 binding protein CRE-BPa X83368 phosphoinositide- 8.7 27.1 3-kinase, catalytic, gamma polypeptide M30269 nidogen (enactin) 8.7 5.5 M91083 chromosome 11 open 8.2 6.6 reading frame 13 D29833 salivary proline- 7.7 5.8 rich protein AB024536 immunoglobulin super- 7.6 8.0 family containing leucine-rich repeat U39400 chromosome 11 open 7.4 7.3 reading frame 4 AF028789 unc119 (C.elegans) 7.4 27.0 homo log NM_003144 signal sequence 7.3 5.9 receptor, alpha (translocon-asso- ciated protein alpha) X52195 arachidonate 5-lipoxy- 7.3 13.1 genase-activating protein U43895 human growth factor- 6.9 6.9 regulated tyrosine kinase substrate L25876 cyclin-dependent 6.7 10.3 kinase inhibitor 3 L04490 NADH dehydrogenase 6.6 11.1 Z18948 S100 calcium-binding 6.3 11.0 protein D10522 myristoylated alanine- 6.1 5.8 rich protein kinase C substrate NM_014442 sialic acid binding 6.1 7.6 Ig-like lectin 8 U81375 solute carrier 6.0 6.4 family 29 AF041410 malignancy-asso- 5.9 5.3 ciated protein U24077 killer cell immuno- 5.8 14.4 globulin-like receptor AL137614 hypothetical protein 4.8 6.8 NM_002406 mannosyl (alpha-1,3-)- 4.7 5.3 glycoprotein beta-1,2- N-acetylglucosaminyl- transferase AB002348 KIAA0350 protein 4.7 7.6 AF165217 tropomodulin 4 (muscle) 4.6 12.3 Z14093 branched chain keto 4.6 5.4 acid dehydrogenase E1, alpha polypeptide U82671 caltractin 3.8 44.5 AL050136 Unknown 3.6 5.0 NM_005135 solute carrier 3.6 5.0 family 12 AK001961 hypothetical protein 3.6 5.9 FLJ11099 AL034410 Unknown 3.2 21.3 S74728 antiquitin 1 3.1 9.2 AL049714 ribosomal protein L34 3.0 19.5 pseudogene 2 NM_014075 PRO0593 protein 2.9 11.5 AF189279 phospholipase A2, 2.8 37.8 group IIE J03925 integrin, alpha M 2.7 9.9 NM_012177 F-box protein Fbx5 2.6 26.2 NM_004519 potassium voltage-gated 2.6 21.1 channel, KQT-like subfamily,member 3 M28825 CD1A antigen, a 2.6 16.8 polypeptide X16940 actin, gamma 2, smooth 2.4 11.8 muscle, enteric X03066 major histocompati- 2.2 36.5 bility complex, class II, DO beta AK001237 hypothetical protein 2.1 18.4 FLJ10375 AB028971 KIAA1048 protein 2.0 9.4 AL137665 Unknown 2.0 7.3

TABLE 56 Polynucleotides Down-regulated by E. coli O111:B4 LPS in A549 Epithelial Cells. E. coli O111:B4 LPS (100 ng/ml) decreased the expression of many polynucleotides in A549 cells as studied by polynucleotide microarrays. LPS was incubated with the A549 cells for 4 h and the RNA was isolated. 5 μg total RNA was used to make Cy3/Cy5 labeled cDNA probes and hybridized onto Human Operon arrays (PRHU04). The Intensity of unstimulated cells is shown in the second column of the Table. The “Ratio: LPS/control” column refers to the intensity of polynucleotide expression in LPS simulated cells divided by in the intensity of unstimulated cells. Control: Accession Media only Ratio: Number Gene Intensity LPS/control NM_017433 myosin IIIA 167.8 0.03 X60484 H4 histone family 36.2 0.04 member E X60483 H4 histone family 36.9 0.05 member D AF151079 hypothetical protein 602.8 0.05 M96843 inhibitor of DNA 30.7 0.05 binding 2, dominant negative helix- loop-helix protein S79854 deiodinase, iodothy- 39.4 0.06 ronine, type III AB018266 matrin 3 15.7 0.08 M33374 NADH dehydrogenase 107.8 0.09 AF005220 Homo sapiens mRNA for 105.2 0.09 NUP98-HOXD13 fusion protein, partial cds Z80783 H2B histone family, 20.5 0.10 member L Z46261 H3 histone family, 9.7 0.12 member A Z80780 H2B histone family, 35.3 0.12 member H U33931 erythrocyte membrane 18.9 0.13 protein band 7.2 (stomatin) M60750 H2B histone family, 35.8 0.14 member A Z83738 H2B histone family, 19.3 0.15 member E Y14690 collagen, type V, 7.5 0.15 alpha 2 M30938 X-ray repair comple- 11.3 0.16 menting defective repair in Chinese hamster cells 5 L36055 eukaryotic trans- 182.5 0.16 lation initiation factor 4E binding protein 1 Z80779 H2B histone family, 54.3 0.16 member G AF226869 5(3)-deoxyribonu- 7.1 0.18 cleotidase; RB- associated KRAB repressor D50924 KIAA0134 gene 91.0 0.18 product AL133415 vimentin 78.1 0.19 AL050179 tropomyosin 1 41.6 0.19 (alpha) AJ005579 RD element 5.4 0.19 M80899 AHNAK nucleo- 11.6 0.19 protein NM_004873 BCL2-associated 6.2 0.19 athanogene 5 X57138 H2A histone family, 58.3 0.20 member N AF081281 lysophos- 7.2 0.22 pholipase I U96759 von Hippel-Lindau 6.6 0.22 binding protein 1 U85977 Human ribosomal 342.6 0.22 protein L12 pseudogene, partial cds D13315 glyoxalase I 7.5 0.22 AC003007 Unknown 218.2 0.22 AB032980 RU2S 246.6 0.22 U40282 integrin-linked 10.1 0.22 kinase U81984 endothelial PAS 4.7 0.23 domain protein 1 X91788 chloride channel, 9.6 0.23 nucleotide- sensitive, 1A AF018081 collagen, type 6.9 0.24 XVIII, alpha 1 L31881 nuclear factor 13.6 0.24 I/X (CCAAT-binding transcription factor) X61123 B-cell trans- 5.3 0.24 location gene 1, anti-proliferative L32976 mitogen-activated 6.3 0.24 protein kinase kinase kinase 11 M27749 immunoglobulin 5.5 0.24 lambda-like poly- peptide 3 X57128 H3 histone family, 9.0 0.25 member C X80907 phosphoinositide- 5.8 0.25 3-kinase, regulatory subunit, polypeptide 2 Z34282 H. sapiens (MAR11) 100.6 0.26 MUC5AC mRNA for mucin (partial) X00089 H2A histone family, 4.7 0.26 member M AL035252 CD39-like 2 4.6 0.26 X95289 PERB11 family member 27.5 0.26 in MHC class I region AJ001340 U3 snoRNP-associated 4.0 0.26 55-kDa protein NM_014161 HSPC071 protein 10.6 0.27 U60873 Unknown 6.4 0.27 X91247 thioredoxin reductase 84.4 0.27 1 AK001284 hypothetical protein 4.2 0.27 FLJ10422 U90840 synovial sarcoma, 6.6 0.27 X breakpoint 3 X53777 ribosomal protein L17 39.9 0.27 AL035067 Unknown 10.0 0.28 AL117665 DKFZP586M1824 protein 3.9 0.28 L14561 ATPase, Ca++ 5.3 0.28 transporting, plasma membrane 1 L19779 H2A histone family, 30.6 0.28 member O AL049782 Unknown 285.3 0.28 X00734 tubulin, beta, 5 39.7 0.29 AK001761 retinoic acid 23.7 0.29 induced 3 U72661 ninjurin 1 4.4 0.29 S48220 deiodinase, iodo- 1,296.1 0.29 thyronine, type I AF025304 EphB2 4.5 0.30 S82198 chymotrypsin C 4.1 0.30 Z80782 H2B histone family, 31.9 0.30 member K X68194 synaptophysin-like 7.9 0.30 protein AB028869 Unknown 4.2 0.30 AK000761 Unknown 4.3 0.30

TABLE 57 Polynucleotides expressed to similar extents after stimulation by the bacterial products LPS, LTA, and CpG DNA. Bacterial products (100 ng/ml S. typhimurium LPS, 1 μg/ml S. aureus LTA or 1 μM CpG) were shown to potently induce the expression of several polynucleotides. Peptide was incubated with the RAW cells for 4 h and the RNA was isolated, converted into labeled cDNA probes and hybridized to Atlas arrays. The intensity of control, unstimulated cells is shown in the second column. The “Ratio LPS/LTA/CpG: Control” column refers to the intensity of polynucleotide expression in bacterial product-simulated cells divided by the intensity of unstimulated cells. Control Ratio Ratio Ratio Accession Unstim. LPS: LTA: CpG: Protein/ number Intensity Control Control Control polynucleotide M15131 20 82 80 55 IL-1β M57422 20 77 64 90 tristetraprolin X53798 20 73 77 78 MIP-2α M35590 188 50 48 58 MIP-1β L28095 20 49 57 50 ICE M87039 20 37 38 45 iNOS X57413 20 34 40 28 TGFβ X15842 20 20 21 15 c-rel proto- oncopolynucleotide X12531 489 19 20 26 MIP-1α U14332 20 14 15 12 IL-15 M59378 580 10 13 11 TNFR1 U37522 151 6 6 6 TRAIL M57999 172 3.8 3.5 3.4 NF-κB U36277 402 3.2 3.5 2.7 I-κB (alpha subunit) X76850 194 3 3.8 2.5 MAPKAP-2 U06924 858 2.4 3 3.2 Stat 1 X14951 592 2 2 2 CD18 X60671 543 1.9 2.4 2.8 NF-2 M34510 5970 1.6 2 1.4 CD14 X51438 2702 1.3 2.2 2.0 vimentin X68932 4455 0.5 0.7 0.5 c-Fms Z21848 352 0.5 0.6 0.6 DNA polymerase X70472 614 0.4 0.6 0.5 B-myb

TABLE 58 Polynucleotides that were differentially regulated by the bacterial products LPS, LTA, and CpG DNA. Bacterial products (100 ng/ml S. typhimurium LPS, 1 μg/ml S. aureus LTA or 1 μM CpG) were shown to potently induce the expression of several polynucleotides. Peptide was incubated with the RAW cells for 4 h and the RNA was isolated, converted into labeled cDNA probes and hybridized to Atlas arrays. The intensity of control, unstimulated cells is shown in the second column. The “Ratio LPS/LTA/CpG: Control” column refers to the intensity of polynucleotide expression in bacterial product-simulated cells divided by the intensity of unstimulated cells. Unstim. Ratio Ratio Ratio Accession Control LPS: LTA: CpG: Protein/ number Intensity Control Control Control polynucleotide X72307 20 1.0 23 1.0 hepatocyte growth factor L38847 20 1.0 21 1.0 hepatoma transmembrane kinase ligand L34169 393 0.3 3 0.5 thrombopoietin J04113 289 1 4 3 Nur77 Z50013 20 7 21 5 H-ras proto- oncopolynucleotide X84311 20 4 12 2 Cyclin A1 U95826 20 5 14 2 Cyclin G2 X87257 123 2 4 1 Elk-1 J05205 20 18 39 20 Jun-D J03236 20 11 19 14 Jun-B M83649 20 71 80 42 Fas 1 receptor M83312 20 69 91 57 CD40L receptor X52264 20 17 23 9 ICAM-1 M13945 573 2 3 2 Pim-1 U60530 193 2 3 3 Mad related protein D10329 570 2 3 2 CD7 X06381 20 55 59 102 Leukemia inhibitory factor (LIF) X70296 20 6.9 13 22 Protease nexin 1 (PN-1) U36340 20 38 7 7 CACCC Box-binding protein BKLF S76657 20 11 6 7 CRE-BPI U19119 272 10 4 4 interferon inducible protein 1

TABLE 59 Confirmation of Table 57 and 58 Array Data. Relative levels Product Untreated LPS LTA CpG CD14^(a) 1.0 2.2 ± 0.4 1.8 + 0.2 1.5 ± 0.3 Vimentin^(a) 1.0 1.2 ± 0.07 1.5 ± 0.05 1.3 ± 0.07 Tristetraprolin^(a) 1.0 5.5 ± 0.5 5.5 ± 1.5 9.5 ± 1.5 LIF^(b) 1.0 2.8 ± 1.2 2.7 ± 0.6 5.1 ± 1.6 NO^(c) 8 ± 1.5  47 ± 2.5  20 ± 3  21 ± 1.5 ^(a)Total RNA was isolated from unstimulated RAW macrophage cells and cells treated for 4 hr with 100 ng/ml S. typhimurium LPS, 1 μg/ml S. aureus LTA, 1 μM CpG DNA or media alone and Northern blots were performed the membrane was probed for GAPDH, CD14, vimetin, and tristetraprolin as described previously [Scott et al]. The hybridization intensities of the Northern blots were compared to GAPDH to look for inconsistencies in loading. These experiments were repeated at least three times and the data shown is the average relative levels of each condition compared to media (as measured by densitometry) ± standard error. ^(b)RAW 264.7 cells were stimulated with 100 ng/ml S. typhimurium LPS, 1 μg/ml S. aureus LTA, 1 μM CpG DNA or media alone for 24 hours. Protein lysates were prepared, run on SDS Page gels and western blots were performed to detect LIF (R & D Systems) These experiments were repeated at least three times and the data shown is the relative levels of LIF compared to media (as measured by densitometry) ± standard error. ^(c)Supernatant was collected from RAW macrophage cells treated with 100 ng/ml S. typhimurium LPS, 1 μg/ml S. aureus LTA, 1 μM CpG DNA, or media alone for 24 hours and tested for the amount of NO formed in the supernatant as estimated from the accumulation of the stable NO metabolite nitrite with the Griess reagent as described previously [Scott, et al]. The data shown is the average of three experiments ± standard error.

TABLE 60 Pattern of Gene expression in A549 Human Epithelial cells up-regulated by bacterial signalling molecules (LPS). E. Coli O111:B4 LPS (100 ng/ml) increased the expression of many polynucleotides in A549 cells as studied by polynucleotide microarrays. LPS was incubated with the A549 cells for 4 h and the RNA was isolated. 5 μg total RNA was used to make Cy3/Cy5 labelled cDNA probes and hybridised onto Human Operon arrays (PRHU04). The example of polynucleotide expression changes in LPS simulated cells represent a greater than 2-fold intensity level change of LPS treated cells from untreated cells. Accession Number Gene AL050337 interferon gamma receptor 1 U05875 interferon gamma receptor 2 NM_002310 leukemia inhibitory factor receptor U92971 coagulation factor II (thrombin) receptor-like 2 Z29575 tumor necrosis factor receptor superfamily member 17 L31584 Chemokine receptor 7 J03925 cAMP response element- binding protein M64788 RAP1, GTPase activating protein NM_004850 Rho-associated kinase 2 D87451 ring finger protein 10 AL049975 Unknown U39067 eukaryotic translation initiation factor 3, subunit 2 AK000942 Unknown AB040057 serine/threonine protein kinase MASK AB020719 KIAA0912 protein AB007856 FEM-1-like death receptor binding protein AL137376 Unknown AL137730 Unknown M90696 cathepsin S AK001143 Unknown AF038406 NADH dehydrogenase AK000315 hypothetical protein FLJ20308 M54915 pim-1 oncogene D29011 proteasome subunit, beta type, 5 AL034348 Unknown D87076 KIAA0239 protein AJ001403 mucin 5, subtype B, tracheobronchial J03925 integrin, alpha M

EXAMPLE 10 Altering Signaling to Protect Against Bacterial Infections

The Salmonella Typhimurium strain SL1344 was obtained from the American Type Culture Collection (ATCC; Manassas, Va.) and grown in Luria-Bertani (LB) broth. For macrophage infections, 10 ml LB in a 125 mL flask was inoculated from a frozen glycerol stock and cultured overnight with shaking at 37° C. to stationary phase. RAW 264.7 cells (1×10⁵ cells/well) were seeded in 24 well plates. Bacteria were diluted in culture medium to give a nominal multiplicity of infection (MOI) of approximately 100, bacteria were centrifuged onto the monolayer at 1000 rpm for 10 minutes to synchronize infection, and the infection was allowed to proceed for 20 min in a 37° C., 5% CO₂ incubator. Cells were washed 3 times with PBS to remove extracellular bacteria and then incubated in DMEM+10% FBS containing 100 μg/ml gentamicin (Sigma, St. Louis, Mo.) to kill any remaining extracellular bacteria and prevent re-infection. After 2 h, the gentamicin concentration was lowered to 10 μg/ml and maintained throughout the assay. Cells were pretreated with inhibitors for 30 min prior to infection at the following concentrations: 50 μM PD 98059 (Calbiochem), 50 μM U 0126 (Promega), 2 mM diphenyliodonium (DPI), 250 μM acetovanillone (apocynin, Aldrich), 1 mM ascorbic acid (Sigma), 30 mM N-acetyl cysteine (Sigma), and 2 mM N^(G)-L-monomethyl arginine (L-NMMA, Molecular Probes) or 2 mM N^(G)-D-monomethyl arginine (D-NMMA, Molecular Probes). Fresh inhibitors were added immediately after infection, at 2 h, and 6-8 h post-infection to ensure potency. Control cells were treated with equivalent volumes of dimethylsulfoxide (DMSO) per mL of media. Intracellular survival/replication of S. Typhimurium SL1344 was determined using the gentamicin-resistance assay, as previously described. Briefly, cells were washed twice with PBS to remove gentamicin, lysed with 1% Triton X-100/0.1% SDS in PBS at 2 h and 24 h post-infection, and numbers of intracellular bacteria calculated from colony counts on LB agar plates. Under these infection conditions, macrophages contained an average of 1 bacterium per cell as assessed by standard plate counts, which permitted analysis of macrophages at 24 h post-infection. Bacterial filiamentation is related to bacterial stress. NADPH oxidase and iNOS can be activated by MEK/ERK signaling. The results (Table 61) clearly demonstrate that the alteration of cell signaling is a method whereby intracellular Salmonella infections can be resolved. Thus since bacteria to up-regulate multiple genes in human cells, this strategy of blocking signaling represents a general method of therapy against infection.

TABLE 61 Effect of the Signaling Molecule MEK on Intracellular Bacteria in IFN-gamma-primed RAW cells. Treatment^(a) Effect^(b) 0 None MEK inhibitor U 0126 Decrease bacterial filamentation (bacterial stress)^(c) Increase in the number of intracellular S. Typhimurium MEK inhibitor PD 98059 Decrease bacterial filamentation (bacterial stress)^(c) Increase in the number of intracellular S. Typhimurium NADPH oxidase inhibitor^(d) Decrease bacterial filamentation (bacterial stress)^(c) Increase in the number of intracellular S. Typhimurium

EXAMPLE 11 Anti-Viral Activity

SDF-1, a C-X-C chemokine is a natural ligand for HIV-1 coreceptor-CXCR4. The chemokine receptors CXCR4 and CCR5 are considered to be potential targets for the inhibition of HIV-1 replication. The crystal structure of SDF-1 exhibits antiparallel β-sheets and a positively charged surface, features that are critical in binding to the negatively charged extracellular loops of CXCR4. These findings suggest that chemokine derivatives, small-size CXCR4 antagonists, or agonists mimicking the structure or ionic property of chemokines may be useful agents for the treatment of X₄ HIV-1 infection. It was found that the cationic peptides inhibited SDF-1 induced T-cell migration suggesting that the peptides may act as CXCR4 antagonists. The migration assays were performed as follows. Human Jurkat T cells were resuspended to 5×10⁶/ml in chemotaxis medium (RPMI 1640/10 mM Hepes/0.5% BSA). Migration assays were performed in 24 well plates using 5 μm polycarbonate Transwell inserts (Costar). Briefly, peptide or controls were diluted in chemotaxis medium and placed in the lower chamber while 0.1 ml cells (5×10⁶/ml) was added to the upper chamber. After 3 hr at 37° C., the number of cells that had migrated into the lower chamber was determined using flow cytometry. The medium from the lower chamber was passed through a FACscan for 30 seconds, gating on forward and side scatter to exclude cell debris. The number of live cells was compared to a “100% migration control” in which 5×10⁵/ml cells had been pipetted directly into the lower chamber and then counted on the FACscan for 30 seconds. The results demonstrate that the addition of peptide results in an inhibition of the migration of Human Jurkat T-cells (Table 62) probably by influencing CXCR4 expression (Tables 63 and 64).

TABLE 62 Peptide inhibits the migration of human Jurkat-T cells: Migration (%) Positive SDF-1 SDF-1 + SEQ 1D1 Negative Experiment control (100 ng/ml) (50 μg/ml) control 1 100% 32% 0% <0.01% 2 100% 40% 0% 0%

TABLE 63 Corresponding polynucleotide array data to Table 56: Polynu- Ratio cleotide/ Polynucleotide Unstimulated peptide: Number Protein Function Intensity Unstimulated Accession CXCR-4 Chemokine 36 4 D87747 receptor

TABLE 64 Corresponding FACs data to Tables 62 and 63: Fold Increase in Concentration Protein Expression Peptide (μg/ml) CXCR-4 SEQ ID NO: 1 10 No change SEQ ID NO: 1 50 1.3 ± 0.03 SEQ ID NO: 1 100 1.6 ± 0.23 SEQ ID NO: 3 100 1.5 ± 0.2 

EXAMPLE 12 Synergistic Combinations

Methods and Materials

S. aureus was prepared in phosphate buffered solution (PBS) and 5% porcine mucin (Sigma) to a final expected concentration of 1-4×10⁷ CFU/ml. 100 μl of S. aureus (mixed with 5% porcine mucin) was injected intraperitoneally (IP) into each CD-1 mouse (6˜8 weeks female weighing 20-25 g (Charles River)). Six hours after the onset of infection, 100 μl of the peptide was injected (50-200 μg total) IP along with 0.1 mg/kg Cefepime. After 24 hours, animals were sacrificed and heart puncture was performed to remove 100 μl of blood. The blood was diluted into 1 ml PBS containing Heparin. This was then further diluted and plated for viable colony counts on Mueller-Hinton agar plates (10⁻¹, 10⁻², 10⁻³, & 10⁻⁴). Viable colonies, colony-forming units (CFU), were counted after 24 hours. Each experiment was carried out a minimum of three times. Data is presented as the average CFU±standard error per treatment group (8-10 mice/group).

Experiments were carried out with peptide and sub-optimal Cefepime given 6 hours after the onset of systemic S. aureus infection (FIG. 1). The data in FIG. 1 is presented as the mean±standard error of viable counts from blood taken from the mice 24 hrs after the onset of infection. The combination of sub optimal antibiotic (cefepime) dosing and SEQ ID NO: 7 resulted in improved therapeutic efficacy. The ability of the peptides to work in combination with sub-optimal concentrations of an antibiotic in a murine infection model is an important finding. It suggests the potential for extending the life of antibiotics in the clinic and reducing incidence of antibiotic resistance.

SEQ ID NO: 1, as an example, induced phosphorylation and activation of the mitogen activated protein kinases, ERK1/2 and p38 in human peripheral blood-derived monocytes and a human bronchial epithelial cell line but not in B- or T-lymphocytes. Phosphorylation was not dependent on the G-protein coupled receptor, FPRL-1, which was previously proposed to be the receptor for SEQ ID NO: 1-induced chemotaxis on human monocytes and T cells. Activation of ERK1/2 and p38 was markedly increased by the presence of granulocyte macrophage-colony stimulating factor (GM-CSF), but not macrophage-colony stimulating factor (M-CSF). Exposure to SEQ ID NO: 1 also led to the activation of Elk-1, a transcription factor that is downstream of and activated by phosphorylated ERK1/2, as well as the up-regulation of various Elk-1 controlled genes. The ability of SEQ ID NO: 1 to signal through these pathways has broad implications in immunity, monocyte activation, proliferation and differentiation.

Methods and Materials

SEQ ID NO: 1 (sequence LLGDFFRKSKEKIGKEFKRIVQRIKDFLRNLVPRTES), was synthesized by Fmoc [(N-(9-fluorenyl) methoxycarbonyl)] chemistry at the Nucleic Acid/Protein Synthesis (NAPS) Unit at UBC. Human recombinant granulocyte-macrophage colony-stimulating factor (GM-CSF), interleukin-4 (IL-4) and macrophage colony-stimulating factor (M-CSF) were purchased from Research Diagnostics Inc. (Flanders, N.J., USA). Pertussis toxin was supplied by List Biological Laboratories Inc. (Campbell, Calif., USA).

Blood monocytes were prepared using standard techniques. Briefly, 100 ml of fresh human venous blood was collected in sodium heparin Vacutainer collection tubes (Becton Dickinson, Mississauga, ON, Canada) from volunteers according to UBC Clinical Research Ethics Board protocol C02-0091. The blood was mixed, at a 1:1 ratio, with RPMI 1640 media [supplemented with 10% v/v fetal calf serum (FBS), 1% L-glutamine, 1 nM sodium pyruvate] in an E-toxa-clean (Sigma-Aldrich, Oakville, ON, Canada) washed, endotoxin-free bottle. PBMC were separated using Ficoll-Paque Plus (Amersham Pharmacia Biotech, Baie D'Urfé, PQ, Canada) at room temperature and washed with phosphate buffered saline (PBS). Monocytes were enriched with the removal of T-cells by rosetting with fresh sheep red blood cells (UBC animal care unit) pre-treated with Vibrio cholerae neuraminidase (Calbiochem Biosciences Inc., La Jolla, Calif., USA) and repeat separation by Ficoll Paque Plus. The enriched monocytes were washed with PBS, then cultured (approximately 2-3×10⁶ per well) for 1 hour at 37° C. followed by the removal of non-adherent cells; monocytes were >95% pure as determined by flow cytometry (data not shown). B-lymphocytes were isolated by removing non-adherent cells and adding them to a new plate for one hour at 37° C. This was repeated a total of three times. Any remaining monocytes adhered to the plates, and residual non-adherent cells were primarily B cells. Cells were cultured in Falcon tissue culture 6-well plates (Becton Dickinson, Mississauga, ON, Canada). The adherent monocytes were cultured in 1 ml media at 37° C. in which SEQ ID NO: 1 and/or cytokines dissolved in endotoxin-free water (Sigma-Aldrich, Oakville, ON, Canada) were added. Endotoxin-free water was added as a vehicle control. For studies using pertussis toxin the media was replaced with 1 ml of fresh media containing 100 ng/ml of toxin and incubated for 60 min at 37° C. SEQ ID NO: 1 and cytokines were added directly to the media containing pertussis toxin. For the isolation of T lymphocytes, the rosetted T cells and sheep red blood cells were resuspended in 20 ml PBS and 10 ml of distilled water was added to lyse the latter. The cells were then centrifuged at 1000 rpm for 5 min after which the supernatant was removed. The pelleted T cells were promptly washed in PBS and increasing amounts of water were added until all sheep red blood cells had lysed. The remaining T cells were washed once in PBS, and viability was confirmed using a 0.4% Trypan blue solution. Primary human blood monocytes and T cells were cultured in RPMI 1640 supplemented with 10% v/v heat-inactivated FBS, 1% v/v L-glutamine, 1 nM sodium pyruvate (GIBCO Invitrogen Corporation, Burlington, ON, Canada). For each experiment between two and eight donors were used.

The simian virus 40-transformed, immortalized 16HBE4o- bronchial epithelial cell line was a generous gift of Dr. D. Gruenert (University of California, San Francisco, Calif.). Cells were routinely cultured to confluence in 100% humidity and 5% CO₂ at 37° C. They were grown in Minimal Essential media with Earles' salts (GIBCO Invitrogen Corporation, Burlington, ON, Canada) containing 10% FBS (Hyclone), 2 mM L-glutamine. For experiments, cells were grown on Costar Transwell inserts (3-μm pore size, Fischer Scientific) in 24-well plates. Cells were seeded at 5×10⁴ cells per 0.25 ml of media on the top of the inserts while 0.95 ml of media was added to the bottom of the well and cultured at 37° C. and 5% CO₂. Transmembrane resistance was measured daily with a Millipore voltohmeter and inserts were used for experiments typically after 8 to 10 days, when the resistance was 500-700 ohms. The cells were used between passages 8 and 20.

Western Immunoblotting

After stimulation, cells were washed with ice-cold PBS containing 1 mM vanadate (Sigma). Next 125 μl of RIPA buffer (50 mM Tris-HCl, pH 7.4, NP-40 1%, sodium deoxycholate 0.25%, NaCl 150 mM, EDTA 1 mM, PMSF 1 mM, Aprotinin, leupeptin, pepstatin 11 g/ml each, sodium orthovanadate 1 mM, NaF 1 mM) was added and the cells were incubated on ice until they were completely lysed as assessed by visual inspection. The lysates were quantitated using a BCA assay (Pierce). 30 μg of lysate was loaded onto 1.5 mm thick gels, which were run at 100 volts for approximately 2 hours. Proteins were transferred to nitrocellulose filters for 75 min at 70 V. The filters were blocked for 2 hours at room temperature with 5% skim milk in TBST (10 mM Tris-HCl pH 8, 150 mM NaCl, 0.1% Tween-20). The filters were then incubated overnight at 4° C. with the anti-ERK1/2-P or anti-p38-P (Cell Signaling Technology, Massachusetts) monoclonal antibodies. Immunoreactive bands were detected using horseradish peroxidase-conjugated sheep anti-mouse IgG antibodies (Amersham Pharmacia, New Jersey) and chemiluminescence detection (Sigma, Missouri). To quantify bands, the films were scanned and then quantified by densitometry using the software program, ImageJ. The blots were reprobed with a β-actin antibody (ICN Biomedical Incorporated, Ohio) and densitometry was performed to allow correction for protein loading.

Kinase Assay

An ERK1/2 activity assay was performed using a non-radioactive kit (Cell Signaling Technology). Briefly, cells were treated for 15 min and lysed in lysis buffer. Equal amounts of proteins were immunoprecipitated with an immobilized phospho-ERK1/2 antibody that reacts only with the phosphorylated (i.e. active) form of ERK1/2. The immobilized precipitated enzymes were then used for the kinase assay using Elk-1 followed by Western blot analysis with antibodies that allow detection and quantitation of phosphorylated substrates.

Quantification of IL-8

Human IL-8 from supernatants of 16HBE40-cells was measured by using the commercially available enzyme-linked immunosorbent assay kit (Biosource) according to the manufacturer's instructions.

Semiquantitative RT-PCR

Total RNA from two independent experiments was isolated from 16HBE4o- cells using RNaqueous (Ambion) as described by the manufacturer. The samples were DNase treated, and then cDNA synthesis was accomplished by using a first-strand cDNA synthesis kit (Gibco). The resultant cDNAs were used as a template in PCRs for various cytokine genes MCP-1 (5′-TCATAGCAGCCACCTTCATTC-3′ (SEQ ID NO:59), 5′-TAGCGCAGATTCTTGGGTTG-3 (SEQ ID NO:60)), MCP-3, (5′-TGTCCTTTCTCAGAGTGGTTCT-3′ (SEQ ID NO:61), 5′-TGCTTCCATAGGGACATCATA-3′ (SEQ ID NO:62)) IL-6, (5′-ACCTGAACCTTCCAAAGATGG-3′ (SEQ ID NO:63), 5′-GCGCAGAATGAGATGAGTTG-3′ (SEQ ID NO:64)), and IL-8, (5′-GTGCAGAGGGTTGTGGAGAAG-3′ (SEQ ID NO:65), 5′-TTCTCCCGTGCAATATCTAGG-3′ (SEQ ID NO:66)) Each RT-PCR reaction was performed in at least duplicate. Results were analysed in the linear phase of amplification and normalized to the housekeeping control, glyceraldehyde-3-phosphate dehydrogenase. Reactions were verified for RNA amplification by including controls without reverse transcriptase.

Results

A. Peptides induce ERK1/2 and p38 phosphorylation in peripheral blood derived monocytes.

To determine if peptide induced the activation of the MAP kinases, ERK1/2 and/or p38, peripheral blood derived monocytes were treated with 50 μg/ml SEQ ID NO: 1 or water (as a vehicle control) for 15 min. To visualize the activated (phosphorylated) form of the kinases, Western blots were performed with antibodies specific for the dually phosphorylated form of the kinases (phosphorylation on Thr202+Tyr204 and Thr180+Tyr182 for ERK1/2 and p38 respectively). The gels were re-probed with an antibody for β-actin to normalize for loading differences. In all, an increase in phosphorylation of ERK1/2 (n=8) and p38 (n=4) was observed in response to SEQ ID NO: 1 treatment (FIG. 2).

FIG. 2 shows exposure to SEQ ID NO: 1 induces phosphorylation of ERK1/2 and p38. Lysates from human peripheral blood derived monocytes were exposed to 50 μg/ml of SEQ ID NO: 1 for 15 minutes. A) Antibodies specific for the phosphorylated forms of ERK and p38 were used to detect activation of ERK1/2 and p38. All donors tested showed increased phosphorylation of ERK1/2 and p38 in response to SEQ ID NO: 1 treatment. One representative donor of eight. Relative amounts of phosphorylation of ERK (B) and p38(C) were determined by dividing the intensities of the phosphorylated bands by the intensity of the corresponding control band as described in the Materials and Methods.

B. Peptide induced activation of ERK1/2 is greater in human serum than in fetal bovine serum.

We were able to demonstrate that LL-37 induced phosphorylation of ERK1/2 did not occur in the absence of serum and the magnitude of phosphorylation was dependent upon the type of serum present such that activation of ERK1/2 was far superior in human serum (HS) than in fetal bovine serum (FBS).

FIG. 3 shows LL-37 induced phosphorylation of ERK1/2 does not occur in the absence of serum and the magnitude of phosphorylation is dependent upon the type of serum present. Human blood derived monocytes were treated with 50 μg/ml of LL-37 for 15 minutes. Lysates were run on a 12% acrylamide gel then transferred to nitrocellulose membrane and probed with antibodies specific for the phosphorylated (active) form of the kinase. To normalize for protein loading, the blots were reprobed with β-actin. Quantification was done with ImageJ software. The FIG. 3 inset demonstrates that LL-37 is unable to induce MAPK activation in human monocytes under serum free conditions. Cells were exposed to 50 mg/ml of LL-37 (+), or endotoxin free water (−) as a vehicle control, for 15 minutes. (A) After exposure to LL-37 in media containing 10% fetal calf serum, phosphorylated ERK1/2 was detectable, however, no phosphorylation of ERK1/2 was detected in the absence of serum (n=3). (B) Elk-1, a transcription factor downstream of ERK1/2, was activated (phosphorylated) upon exposure to 50 μg/ml of LL-37 in media containing 10% fetal calf serum, but not in the absence of serum (n=2).

C. Peptide induced activation of ERK1/2 and p38 is dose dependent and demonstrates synergy with GM-CSF.

GM-CSF, IL-4, or M-CSF (each at 100 ng/ml) was added concurrently with SEQ ID NO: 1 and phosphorylation of ERK1/2 was measured in freshly isolated human blood monocytes. ERK1/2 phosphorylation was evident when cells were treated with 50 μg/ml of SEQ ID NO: 1 (8.3 fold increase over untreated, n=9) but not at lower concentrations (n=2). In the presence of 100 ng/ml GM-CSF, SEQ ID NO: 1-induced ERK1/2 phosphorylation increased markedly (58 fold greater than untreated, n=5). Furthermore, in the presence of GM-CSF, activation of ERK1/2 occurred in response to concentrations of 5 and 10 μg/ml of SEQ ID NO: 1, respectively, in the two donors tested (FIG. 4). This demonstrates that SEQ ID NO: 1 induced activation of ERK1/2 occurred at a lower threshold in the presence of GM-CSF, a cytokine found locally at sites of infection.

FIG. 4 shows LL-37 induced activation of ERK1/2 occurs at lower concentrations and is amplified in the presence of certain cytokines. When freshly isolated monocytes were stimulated in media containing both GM-CSF (100 ng/ml) and IL-4 (100 ng/ml) LL-37 induced phosphorylation of ERK1/2 was apparent at concentrations as low as 5 μg/ml. This synergistic activation of ERK1/2 seems to be due primarily to GM-CSF.

D. Activation of ERK1/2 leads to transcription of Elk-1 controlled genes and secretion of IL-8

IL-8 release is governed, at least in part, by activation of the ERK1/2 and p38 kinases. In order to determine if peptide could induce IL-8 secretion the human bronchial cell line, 16HBE4o-, was grown to confluency in Transwell filters, which allows for cellular polarization with the creation of distinct apical and basal surfaces. When the cells were stimulated with 50 μg/ml of SEQ ID NO: 1 on the apical surface for four hours a statistically significant increase in the amount of IL-8 released into the apical supernatant was detected (FIG. 5). To determine the downstream transcriptional effects of peptide-induced MAP kinase activation, the expression of genes known to be regulated by ERK1/2 or p38 was assessed by RT-PCR. RT-PCR was performed on RNA isolated from 16HBE4o- cells, treated for four hours with 50 μg/ml of SEQ ID NO: 1 in the presence of serum, from two independent experiments. MCP-1 and IL-8 have been demonstrated to be under the transcriptional control of both ERK1/2 and p38, consistent with this they are up-regulated 2.4 and 4.3 fold respectively. Transcription of MCP-3 has not previously been demonstrated to be influenced by the activation of the mitogen activated protein kinases, consistent with this, expression is not affected by peptide treatment. (FIG. 5). These data are consistent with the hypothesis that activation of the activation of the ERK1/2 and p38 signaling pathways has functional effects on transcription of cytokine genes with immunomodulatory functions. The inset to FIG. 3B also demonstrates that peptide induced the phosphorylation of transcription factor Elk-1 in a serum dependent manner.

FIG. 5 shows peptide affects both transcription of various cytokine genes and release of IL-8 in the 16HBE4o- human bronchial epithelial cell line. Cells were grown to confluency on a semi-permeable membrane and stimulated on the apical surface with 50 μg/ml of SEQ ID NO: 1 for four hours. A) SEQ ID NO: 1 treated cells produced significantly more IL-8 than controls, as detected by ELISA in the supernatant collected from the apical surface, but not from the basolateral surface. Mean±SE of three independent experiments shown, asterisk indicates p=0.002. B) RNA was collected from the above experiments and RT-PCR was performed. A number of cytokine genes known to be regulated by either ERK1/2 or p38 were up-regulated upon stimulation with peptide. The average of two independent experiments is shown.

Although the invention has been described with reference to the presently preferred embodiment, it should be understood that various modifications can be made without departing from the spirit of the invention. Accordingly, the invention is limited only by the following claims. 

1. A method of treating inflammation in a subject having or at risk of having inflammation comprising administering to the subject a therapeutically effective amount of the peptide as set forth in SEQ ID NO:7.
 2. The method of claim 1, wherein the peptide contains at least one amino acid that is a D-enantiomer.
 3. The method of claim 1, wherein the peptide is cyclic.
 4. The method of claim 1, wherein the peptide sequence is reversed.
 5. The method of claim 1, wherein the peptide is administered in combination with an antibiotic.
 6. The method of claim 1, wherein the peptide is administered in combination with granulocyte-macrophage colony stimulating factor (GM-CSF).
 7. The method of claim 5, wherein the antibiotic is selected from aminoglycosides, penicillins, cephalosporins, cerbacephems, cephamycins, chloramphenicols, glycylcyclines, licosamides, aminocyclitols, cationic antimicrobial peptides, lipopeptides, poymyxins, streptogramins, oxazoladinones, lincosamides, fluoroquinolones, carbapenems, tetracyclines, macrolides, beta-lactams carbapenems, monobactams, quinolones, tetracyclines, or glycopeptides.
 8. A method of treating sepsis in a subject having or at risk of having sepsis comprising administering to the subject a therapeutically effective amount of the peptide as set forth in SEQ ID NO:7.
 9. The method of claim 8, wherein the peptide contains at least one amino acid that is a D-enantiomer.
 10. The method of claim 8, wherein the peptide is cyclic.
 11. The method of claim 8, wherein the peptide sequence is reversed.
 12. The method of claim 8, wherein the peptide is administered in combination with an antibiotic.
 13. The method of claim 8, wherein the peptide is administered in combination with granulocyte-macrophage colony stimulating factor (GM-CSF).
 14. The method of claim 12, wherein the antibiotic is selected from aminoglycosides, penicillins, cephalosporins, cerbacephems, cephamycins, chioramphenicols, glycylcyclines, licosamides, aminocyclitols, cationic antimicrobial peptides, lipopeptides, poymyxins, streptogramins, oxazoladinones, lincosamides, fluoroquinolones, carbapenems, tetracyclines, macrolides, beta-lactams carbapenems, monobactams, quinolones, tetracyclines, or glycopeptides. 